archaeopteryx 2.3.2 → 3.1.0

package/forester.js

@@ -7,7 +7,7 @@
  *  This library is free software; you can redistribute it and/or
  *  modify it under the terms of the GNU Lesser General Public
  *  License as published by the Free Software Foundation; either
- *  version 2.1 of the License, or (at your option) any later version.
+ *  version 3 of the License, or (at your option) any later version.
  *
  *  This library is distributed in the hope that it will be useful,
  *  but WITHOUT ANY WARRANTY; without even the implied warranty of
@@ -15,13 +15,13 @@
  *  Lesser General Public License for more details.
  *
  *  You should have received a copy of the GNU Lesser General Public
- *  License along with this library; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ *  License along with this library; if not, see
+ *  <https://www.gnu.org/licenses/>.
  *
  */
 
-// v 2.3.2
-// 2026-04-22
+// v 3.1.0
+// 2026-09-04
 //
 // forester.js is a general suite for dealing with phylogenetic trees.
 // 
@@ -74,34 +74,6 @@
 
     const NUMBERS_ONLY_PATTERN = /^[-+]?[0-9\\.]+$/;
 
-    const MSA_RESIDUE_SORT_MAP = new Map();
-    MSA_RESIDUE_SORT_MAP.set('A', 0);
-    MSA_RESIDUE_SORT_MAP.set('C', 1);
-    MSA_RESIDUE_SORT_MAP.set('D', 2);
-    MSA_RESIDUE_SORT_MAP.set('E', 3);
-    MSA_RESIDUE_SORT_MAP.set('F', 4);
-    MSA_RESIDUE_SORT_MAP.set('G', 5);
-    MSA_RESIDUE_SORT_MAP.set('H', 6);
-    MSA_RESIDUE_SORT_MAP.set('I', 7);
-    MSA_RESIDUE_SORT_MAP.set('K', 8);
-    MSA_RESIDUE_SORT_MAP.set('L', 9);
-    MSA_RESIDUE_SORT_MAP.set('M', 10);
-    MSA_RESIDUE_SORT_MAP.set('N', 11);
-    MSA_RESIDUE_SORT_MAP.set('P', 12);
-    MSA_RESIDUE_SORT_MAP.set('Q', 13);
-    MSA_RESIDUE_SORT_MAP.set('R', 14);
-    MSA_RESIDUE_SORT_MAP.set('S', 15);
-    MSA_RESIDUE_SORT_MAP.set('T', 16);
-    MSA_RESIDUE_SORT_MAP.set('U', 17);// Uracil
-    MSA_RESIDUE_SORT_MAP.set('V', 18);
-    MSA_RESIDUE_SORT_MAP.set('W', 19);
-    MSA_RESIDUE_SORT_MAP.set('Y', 20);
-    MSA_RESIDUE_SORT_MAP.set('B', 21);// Asparagine or aspartic acid
-    MSA_RESIDUE_SORT_MAP.set('Z', 22);// Glutamine or glutamic acid
-    MSA_RESIDUE_SORT_MAP.set('X', 23);
-    MSA_RESIDUE_SORT_MAP.set('?', 24);
-    MSA_RESIDUE_SORT_MAP.set('-', 25);
-    MSA_RESIDUE_SORT_MAP.set('.', 26);
 
 
     /**
@@ -222,43 +194,6 @@
     };
 
 
-    forester.filterByNodeProperty = function (positive, phy, propertyMap) {
-        if (!phy) {
-            throw ("cannot delete null tree");
-        }
-        if (!propertyMap) {
-            throw ("property list is null");
-        }
-        const toDelete = [];
-        forester.preOrderTraversalAll(phy, function (n) {
-            if (!n.children && !n._children) {
-                if (n.properties && n.properties.length > 0) {
-                    const propertiesLength = n.properties.length;
-                    for (let i = 0; i < propertiesLength; ++i) {
-                        const property = n.properties[i];
-                        if (property.ref && property.value && property.applies_to === 'node') {
-                            if (positive) {
-                                if (property.ref in propertyMap && !propertyMap[property.ref].includes(property.value)) {
-                                    toDelete.push(n);
-                                }
-                            } else {
-                                if (property.ref in propertyMap && propertyMap[property.ref].includes(property.value)) {
-                                    toDelete.push(n);
-                                }
-                            }
-                        }
-                    }
-                }
-            }
-        });
-        const l = toDelete.length;
-        console.log(toDelete);
-        for (let i = 0; i < l; ++i) {
-            forester.deleteSubtree(phy, toDelete[i]);
-        }
-    };
-
-
     /**
      * To delete a sub-tree or external node.
      *
@@ -607,15 +542,6 @@
         }
     };
 
-    forester.unCollapseAll = function (node) {
-        forester.preOrderTraversal(node, function (d) {
-            if (d._children) {
-                d.children = d._children;
-                d._children = null;
-            }
-        });
-    };
-
     forester.copyBranchData = function (nodeFrom, nodeTo) {
         nodeTo.width = nodeFrom.width;
         nodeTo.color = nodeFrom.color;
@@ -658,216 +584,722 @@
         return s / l;
     };
 
-    forester.setToArray = function (set) {
-        let array = [];
-        if (set) {
-            set.forEach(function (e) {
-                array.push(e);
-            });
+
+    // ------------------------------------------------------------------
+    // Automatic visualization candidates
+    // ------------------------------------------------------------------
+    //
+    // Decides, from the tree alone, which of its elements are worth offering
+    // as a Color, Color-range, or Shape visualization. This replaces the old
+    // caller-supplied "nodeVisualizations" configuration: the tree is the
+    // only input.
+    //
+    // Only external nodes are considered; the domains always come from the
+    // COMPLETE tree, so a value keeps its colour inside a subtree view even
+    // when the subtree does not contain it.
+    //
+    // Candidates: taxonomy code / scientific name / common name, sequence
+    // name / symbol / gene name, and node properties (applies_to "node").
+    // The "style:" namespace is never a candidate -- the desktop reserves it
+    // for per-node rendering instructions (font_color, node_shape, ...), so
+    // treating it as data would mean colouring by a colour.
+    //
+    // The rules, tuned against the real ViPR / BV-BRC trees in docs/data
+    // (which test/visualization_test.js holds as executable fixtures):
+    //
+    //   coverage    present on >= 2/3 of the external nodes. Database
+    //               exports are always patchy -- demanding 100% would
+    //               reject nearly every field of the BV-BRC trees while a
+    //               field on 9% of nodes (state_province) says nothing.
+    //               Nodes without a value simply keep the default look.
+    //   repetition  at least 2 distinct values (1 paints the whole tree
+    //               alike), and fewer distinct values than external nodes
+    //               (all-unique means identifiers).
+    //   categorical <= 20 distinct values -> Color. Above ~12 the reader
+    //               leans on the legend, but the real trees cluster at
+    //               15-17 (host names, countries, taxonomy codes).
+    //   wide        21+ distinct values are still offered -- as the desktop
+    //               does, every value gets a colour and the LEGEND caps the
+    //               display -- but only when values genuinely repeat:
+    //               distinct/covered <= 0.6, or near-unique fields (strains,
+    //               species names, dates) would flood the menus. Wide fields
+    //               rank after everything else and are never auto-applied.
+    //   numeric     every value parses as a finite number. Up to 10 distinct
+    //               values default to individual colours -- numbers that few
+    //               are usually codes (HA/NA subtypes), and ten is what the
+    //               palette's strong first half holds -- 11 to 20 default to
+    //               a Color-range, and both of those may be switched in the
+    //               legend; above 20 it is a range with no switch. Guard:
+    //               distinct/covered <= 0.9, or "numeric" identifiers
+    //               (genome ids) would become ramps.
+    //   shape       <= 7 distinct values (d3 v7 has exactly 7 distinct
+    //               fill symbols), numeric or not -- two years as two
+    //               shapes is genuinely useful.
+    //   multi-value a ref carried more than once by any external node is
+    //               not a candidate: a node cannot be two colours, and
+    //               picking one silently is worse than not offering it.
+    //
+    const VIS_MIN_COVERAGE_NUM = 2;    // coverage >= 2/3, held as a
+    const VIS_MIN_COVERAGE_DEN = 3;    // fraction so the test is integer-exact
+    const VIS_MAX_COLOR_CATEGORIES = 20;
+    const VIS_MAX_SHAPE_CATEGORIES = 7;
+    const VIS_NUMERIC_CATEGORY_MAX = 10;   // <= this many distinct numbers -> colours by default
+    const VIS_WIDE_REPEAT_NUM = 3;         // wide categorical: distinct/covered <= 0.6,
+    const VIS_WIDE_REPEAT_DEN = 5;         // held integer-exact
+    const VIS_MAX_NUMERIC_UNIQUE_NUM = 9;    // distinct/covered <= 0.9,
+    const VIS_MAX_NUMERIC_UNIQUE_DEN = 10;   // integer-exact as well
+    const VIS_EXCLUDED_REF_PREFIX = 'style:';
+    // Refs that are never a visualization, however their values distribute.
+    // A taxon identifier repeats like a category and passes every statistical
+    // test above, yet says nothing a colour could carry that the species name
+    // beside it does not -- and reads as "11320" in a legend. Matched on the
+    // ref's local name with case and separators ignored, so vipr:NCBI_Taxon_Id,
+    // ncbi_taxid, taxon_id and taxonomy_id all count.
+    const VIS_EXCLUDED_LOCAL_NAME_RE = /(taxonomy|taxon|tax)id$/;
+
+    function visExcludedRef(ref) {
+        if (ref.indexOf(VIS_EXCLUDED_REF_PREFIX) === 0) {
+            return true;
         }
-        return array;
+        let local = ref.substring(ref.indexOf(':') + 1).toLowerCase().replace(/[^a-z0-9]/g, '');
+        return VIS_EXCLUDED_LOCAL_NAME_RE.test(local);
+    }
+
+    // ---- display normalization --------------------------------------------
+    //
+    // Property values are grouped for colouring after a normalization pass,
+    // following the desktop's PropertyColorScheme with two deliberate
+    // extensions. The desktop's part: values are trimmed, underscores read as
+    // spaces, whitespace runs collapse, grouping is case-insensitive, and for
+    // refs literally named "host" / "country" a trailing qualifier is cut
+    // (everything from the first ';' / ':' -- "USA:CA" groups as "USA",
+    // "Homo sapiens; sex: M" as "Homo sapiens"). Our extensions, chosen for a
+    // VISUALIZATION tool that should look good on the data it is given: a
+    // small dictionary of common-animal synonyms folds scientific names and
+    // spelling variants into one capitalized common name ("bovine", "calf",
+    // "cattle" and "Bos taurus" are all Cow -- including "Human", where the
+    // desktop folds the other way); and a qualifier cut that would leave an
+    // unclosed "(" behind is trimmed back to before it, so
+    // "Saimiri boliviensis (squirrel monkey; voucher: X)" reads as
+    // "Saimiri boliviensis" rather than dangling.
+    //
+    // Matching is WHOLE-VALUE only (after a trailing parenthetical is tried
+    // stripped: "Bos taurus (cattle)" looks up "bos taurus") -- never by
+    // substring, so "ferret badger" (a Melogale, not a ferret) and
+    // "42-day-old pig" keep their own rows. The dictionary applies to
+    // property fields only; taxonomy and sequence elements are curated text
+    // and stay verbatim. Node names, exports, search, and the node-data
+    // dialog always show the raw values -- this is display grouping, nothing
+    // more.
+    // CROSS-IMPLEMENTATION CONTRACT with desktop Archaeopteryx: this
+    // dictionary is carried verbatim on both sides (as agreed with the
+    // desktop's Color-by parity work), so a value groups the same way in
+    // both viewers. Extend BOTH implementations together, never just one.
+    const VIS_SYNONYMS = {
+        'Human': ['humans', 'homo sapiens', 'h. sapiens'],
+        'Cow': ['bovine', 'calf', 'cattle', 'bull', 'heifer', 'bos taurus', 'b. taurus'],
+        'Chicken': ['broiler chicken', 'broiler', 'hen', 'rooster', 'gallus gallus', 'g. gallus', 'gallus gallus domesticus'],
+        'Mouse': ['house mouse', 'murine', 'mus musculus', 'm. musculus'],
+        'Rat': ['brown rat', 'norway rat', 'black rat', 'rattus norvegicus', 'r. norvegicus', 'rattus rattus'],
+        'Ferret': ['domestic ferret', 'mustela putorius furo', 'mustela furo', 'm. putorius furo'],
+        'Guinea pig': ['cavy', 'domestic guinea pig', 'cavia porcellus', 'c. porcellus'],
+        'Rhesus monkey': ['rhesus macaque', 'macaca mulatta', 'm. mulatta'],
+        'Rabbit': ['european rabbit', 'oryctolagus cuniculus', 'o. cuniculus'],
+        'Dog': ['canine', 'canis familiaris', 'canis lupus familiaris', 'c. familiaris'],
+        'Cat': ['feline', 'domestic cat', 'felis catus', 'f. catus', 'felis silvestris catus'],
+        'Duck': ['mallard', 'mallard duck', 'domestic duck', 'anas platyrhynchos', 'a. platyrhynchos'],
+        'Pig': ['swine', 'porcine', 'hog', 'piglet', 'sus scrofa', 's. scrofa', 'sus scrofa domesticus'],
+        'Horse': ['equine', 'mare', 'stallion', 'equus caballus', 'e. caballus'],
+        'Sheep': ['ovine', 'lamb', 'ewe', 'ovis aries', 'o. aries'],
+        'Goat': ['caprine', 'capra hircus', 'c. hircus'],
+        'Camel': ['dromedary', 'bactrian camel', 'camelus dromedarius', 'camelus bactrianus', 'c. dromedarius']
     };
+    // null prototype: the lookup is keyed by FILE values, and a value named
+    // "toString" / "__proto__" must miss, not return an inherited member
+    // (that crashed visualizationCandidates -- and so launch -- outright)
+    const VIS_SYNONYM_LOOKUP = Object.create(null);
+    Object.keys(VIS_SYNONYMS).forEach(function (canon) {
+        VIS_SYNONYM_LOOKUP[canon.toLowerCase()] = canon;
+        VIS_SYNONYMS[canon].forEach(function (syn) {
+            VIS_SYNONYM_LOOKUP[syn] = canon;
+        });
+    });
+
+    // ';' for host fields, ':' for country fields, null otherwise -- matched
+    // on the ref's local name EXACTLY, so host_group and isolation_country
+    // keep their full values.
+    function visQualifierCut(ref) {
+        let i = ref.lastIndexOf(':');
+        let local = (i >= 0 ? ref.substring(i + 1) : ref).toLowerCase();
+        if (local === 'country') {
+            return ':';
+        }
+        if (local === 'host') {
+            return ';';
+        }
+        return null;
+    }
 
-    forester.setToSortedArray = function (set) {
-        let array = [];
-        if (set) {
-            set.forEach(function (e) {
-                array.push(e);
-            });
+    // The display form a raw property value is grouped under (case is
+    // preserved here; grouping lowercases it).
+    function visDisplayLabel(value, cut) {
+        let s = value;
+        if (cut) {
+            let at = s.indexOf(cut);
+            if (at >= 0) {
+                s = s.substring(0, at);
+                // the cut may land inside a parenthetical; trim back to
+                // before the first unclosed '('
+                let open = [];
+                for (let i = 0; i < s.length; ++i) {
+                    if (s.charAt(i) === '(') {
+                        open.push(i);
+                    } else if (s.charAt(i) === ')') {
+                        open.pop();
+                    }
+                }
+                if (open.length > 0) {
+                    s = s.substring(0, open[0]);
+                }
+            }
         }
-        return array.sort();
+        // the trailing trim matters: without it, a value that is ALL
+        // underscores (e.g. "_") folds to a single space rather than empty,
+        // so it survives the caller's empty-string drop; "_cat_" folds to
+        // " cat " and never joins the "cat" group. (The leading trim alone
+        // only catches whitespace that was already there before folding.)
+        s = s.trim().replace(/_/g, ' ').replace(/\s+/g, ' ').trim();
+        let hit = VIS_SYNONYM_LOOKUP[s.toLowerCase()];
+        if (!hit) {
+            let stripped = s.replace(/\s*\([^()]*\)\s*$/, '');
+            if (stripped !== s && stripped.length > 0) {
+                hit = VIS_SYNONYM_LOOKUP[stripped.toLowerCase()];
+            }
+        }
+        return hit || s;
+    }
+
+    // Fixed candidate slots for the phyloXML elements (properties use their
+    // ref). CROSS-IMPLEMENTATION CONTRACT with desktop Archaeopteryx: the
+    // ids here (tax:code, seq:name, ...) and the rule that taxonomy/sequence
+    // elements stay VERBATIM (never folded/grouped like property values,
+    // see visDisplayLabel above) are pinned on both sides. Extend BOTH
+    // implementations together, never just one.
+    const VIS_ELEMENT_SLOTS = [
+        {id: 'tax:code', kind: 'taxonomy', label: 'Taxonomy Code', get: function (t) { return t.code; }},
+        {id: 'tax:scientific_name', kind: 'taxonomy', label: 'Scientific Name', get: function (t) { return t.scientific_name; }},
+        {id: 'tax:common_name', kind: 'taxonomy', label: 'Common Name', get: function (t) { return t.common_name; }},
+        {id: 'seq:name', kind: 'sequence', label: 'Sequence Name', get: function (s) { return s.name; }},
+        {id: 'seq:symbol', kind: 'sequence', label: 'Sequence Symbol', get: function (s) { return s.symbol; }},
+        {id: 'seq:gene_name', kind: 'sequence', label: 'Gene Name', get: function (s) { return s.gene_name; }}
+    ];
+
+    // "geographic_group" reads like a database column; a menu should say
+    // "Geographic Group". Underscores become spaces, camelCase is split
+    // (FluSeason -> Flu Season, GlobalH1Clade -> Global H1 Clade), and
+    // all-lowercase words are capitalized. Words that already carry capitals
+    // (PANGO, HA, H5N1) are left exactly as written.
+    function prettifyVisLabel(name) {
+        return name
+            .replace(/_/g, ' ')
+            .replace(/([a-z])([A-Z])/g, '$1 $2')
+            .replace(/([0-9])([A-Z][a-z])/g, '$1 $2')
+            .split(' ')
+            .map(function (w) {
+                return /^[a-z]/.test(w) ? w.charAt(0).toUpperCase() + w.substring(1) : w;
+            })
+            .join(' ');
+    }
+
+    // The display name for a property ref, as the Color-by menu and legends
+    // show it: namespace dropped, then prettified. Exported so the node-data
+    // dialog names a property the same way the rest of the viewer does.
+    forester.propertyDisplayName = function (ref) {
+        let local = ref.indexOf(':') >= 0 ? ref.substring(ref.indexOf(':') + 1) : ref;
+        return prettifyVisLabel(local);
     };
 
-    forester.calcMinMaxInSet = function (set) {
-        let array = [];
-        let first = true;
-        let min = 0;
-        let max = 0;
-        if (set) {
-            set.forEach(function (e) {
-                e = parseFloat(e);
-                if (first) {
-                    first = false;
-                    min = e;
-                    max = e;
-                } else {
-                    if (e < min) {
-                        min = e;
+    forester.visualizationCandidates = function (tree) {
+        let total = 0;
+        let stats = Object.create(null);   // id -> {kind, ref, label, nodes, values:Set, multi}; null-proto: ids embed file refs
+
+        forester.preOrderTraversalAll(tree, function (n) {
+            if (n.children || n._children) {
+                return;
+            }
+            total++;
+            // gather this node's values per candidate id first, so carrying
+            // the same ref twice is visible as such
+            let perNode = Object.create(null);
+            function add(id, kind, ref, label, value) {
+                if (value === undefined || value === null) {
+                    return;
+                }
+                let v = String(value).trim();
+                if (v.length === 0) {
+                    return;
+                }
+                if (!perNode[id]) {
+                    perNode[id] = {kind: kind, ref: ref, label: label, values: []};
+                }
+                perNode[id].values.push(v);
+            }
+            VIS_ELEMENT_SLOTS.forEach(function (slot) {
+                let list = slot.kind === 'taxonomy' ? n.taxonomies : n.sequences;
+                if (list) {
+                    for (let i = 0; i < list.length; ++i) {
+                        add(slot.id, slot.kind, null, slot.label, slot.get(list[i]));
+                    }
+                }
+            });
+            if (n.properties) {
+                for (let i = 0; i < n.properties.length; ++i) {
+                    let p = n.properties[i];
+                    if (p.ref && p.applies_to === 'node' && !visExcludedRef(p.ref)) {
+                        add('prop:' + p.ref, 'property', p.ref, null, p.value);
+                    }
+                }
+            }
+            Object.keys(perNode).forEach(function (id) {
+                let g = perNode[id];
+                if (!stats[id]) {
+                    stats[id] = {kind: g.kind, ref: g.ref, label: g.label,
+                        cut: g.kind === 'property' ? visQualifierCut(g.ref) : null,
+                        nodes: 0, keys: Object.create(null), multi: false};
+                }
+                let s = stats[id];
+                s.nodes++;
+                if (g.values.length > 1) {
+                    s.multi = true;
+                }
+                for (let i = 0; i < g.values.length; ++i) {
+                    // properties group under their normalized display form;
+                    // taxonomy / sequence elements are curated text, verbatim
+                    let display = g.kind === 'property' ? visDisplayLabel(g.values[i], s.cut) : g.values[i];
+                    if (display.length === 0) {
+                        continue;
                     }
-                    if (e > max) {
-                        max = e;
+                    let key = g.kind === 'property' ? display.toLowerCase() : display;
+                    if (!s.keys[key]) {
+                        s.keys[key] = {count: 0, spellings: Object.create(null)};
                     }
+                    s.keys[key].count++;
+                    s.keys[key].spellings[display] = (s.keys[key].spellings[display] || 0) + 1;
                 }
             });
-        }
-        array[0] = min;
-        array[1] = max;
-        return array;
-    };
+        });
 
-    forester.calcMinMeanMaxInSet = function (set) {
-        let array = [];
-        let first = true;
-        let min = 0;
-        let max = 0;
-        let mean = 0;
-        let sum = 0;
-        let n = 0;
-        if (set) {
-            set.forEach(function (e) {
-                e = parseFloat(e);
-                ++n;
-                sum += e;
-                if (first) {
-                    first = false;
-                    min = e;
-                    max = e;
-                } else {
-                    if (e < min) {
-                        min = e;
+        let candidates = [];
+        Object.keys(stats).forEach(function (id) {
+            let s = stats[id];
+            if (s.multi) {
+                return;
+            }
+            let covered = s.nodes;
+            // one legend row per group: the dictionary canonical where one
+            // applied (it is then the only recorded spelling), otherwise the
+            // most frequent raw spelling (ties alphabetically), capitalized
+            let canon = Object.create(null);
+            let counts = Object.create(null);
+            Object.keys(s.keys).forEach(function (key) {
+                let group = s.keys[key];
+                let rep = null;
+                let best = -1;
+                Object.keys(group.spellings).forEach(function (spelling) {
+                    let n = group.spellings[spelling];
+                    if (n > best || (n === best && spelling < rep)) {
+                        rep = spelling;
+                        best = n;
                     }
-                    if (e > max) {
-                        max = e;
+                });
+                if (s.kind === 'property') {
+                    rep = rep.charAt(0).toUpperCase() + rep.substring(1);
+                }
+                canon[key] = rep;
+                counts[rep] = group.count;
+            });
+            let distinct = Object.keys(canon).length;
+            if (covered * VIS_MIN_COVERAGE_DEN < total * VIS_MIN_COVERAGE_NUM) {
+                return;
+            }
+            if (distinct < 2) {
+                return;
+            }
+            let values = Object.keys(counts);
+            let numeric = values.every(function (v) {
+                return Number.isFinite(Number(v));
+            });
+            let colorMode;
+            let switchable = false;
+            let wide = false;
+            if (numeric) {
+                if (distinct * VIS_MAX_NUMERIC_UNIQUE_DEN > covered * VIS_MAX_NUMERIC_UNIQUE_NUM) {
+                    return;
+                }
+                colorMode = distinct <= VIS_NUMERIC_CATEGORY_MAX ? 'category' : 'range';
+                switchable = distinct <= VIS_MAX_COLOR_CATEGORIES;
+                values.sort(function (a, b) {
+                    return Number(a) - Number(b);
+                });
+            } else {
+                if (distinct >= total) {
+                    return;
+                }
+                if (distinct > VIS_MAX_COLOR_CATEGORIES) {
+                    if (distinct * VIS_WIDE_REPEAT_DEN > covered * VIS_WIDE_REPEAT_NUM) {
+                        return;
                     }
+                    wide = true;
                 }
+                colorMode = 'category';
+                values.sort();
+            }
+            // Rank by how much a visualization would actually show: coverage
+            // times balance, where balance is the normalized entropy of the
+            // value distribution. A field that is one value on 92% of nodes
+            // scores low even with full coverage; an even 4-way split on 90%
+            // of nodes scores high.
+            let entropy = 0;
+            values.forEach(function (v) {
+                let p = counts[v] / covered;
+                entropy -= p * Math.log(p);
             });
-        }
-        if (n > 0) {
-            mean = sum / n;
-        }
-        array[0] = min;
-        array[1] = mean;
-        array[2] = max;
-        return array;
-    };
+            let balance = entropy / Math.log(distinct);
+            candidates.push({
+                id: id,
+                kind: s.kind,
+                ref: s.ref,
+                // property labels drop the namespace prefix and are prettified;
+                // a cross-namespace collision is resolved below by restoring
+                // the full ref verbatim
+                label: s.label || prettifyVisLabel(s.ref.indexOf(':') >= 0 ? s.ref.substring(s.ref.indexOf(':') + 1) : s.ref),
+                numeric: numeric,
+                coverage: covered,
+                total: total,
+                values: values,
+                counts: counts,
+                canon: s.kind === 'property' ? canon : null,
+                cut: s.cut,
+                score: (covered / total) * balance,
+                colorMode: colorMode,
+                switchable: switchable,
+                wide: wide,
+                shape: distinct <= VIS_MAX_SHAPE_CATEGORIES
+            });
+        });
 
+        let labelCount = Object.create(null);
+        candidates.forEach(function (c) {
+            labelCount[c.label] = (labelCount[c.label] || 0) + 1;
+        });
+        candidates.forEach(function (c) {
+            if (labelCount[c.label] > 1 && c.ref) {
+                c.label = c.ref;
+            }
+        });
 
-    /**
-     * This collects all properties in a tree
-     * and returns them as dictionary of Sets mapping
-     * keys to values.
-     * It only collects properly formed properties
-     * (as per phyloXML standard), which means
-     * that 'applies_to' and 'datatype' have to be present.
-     *
-     *
-     * @param phy - A phyloXML-based tree object or node.
-     * @param appliesTo - 'phylogeny', 'clade', 'node', 'annotation', 'parent_branch', or 'other'.
-     * @param externalOnly - To collect from external nodes only.
-     * @returns {{}}
-     */
-    forester.collectProperties = function (phy, appliesTo, externalOnly) {
-        let props = {};
-        forester.preOrderTraversalAll(phy, function (n) {
+        // Best first: clean categorical fields, then numeric ranges, then the
+        // wide categoricals (offered, never leading) -- within each tier by
+        // score, ties alphabetically. The first entry is what the viewer
+        // applies on load.
+        function tierOf(c) {
+            if (c.colorMode === 'category') {
+                return c.wide ? 2 : 0;
+            }
+            return 1;
+        }
+        candidates.sort(function (a, b) {
+            let ta = tierOf(a);
+            let tb = tierOf(b);
+            if (ta !== tb) {
+                return ta - tb;
+            }
+            if (a.score !== b.score) {
+                return b.score - a.score;
+            }
+            let la = a.label.toLowerCase();
+            let lb = b.label.toLowerCase();
+            return la < lb ? -1 : (la > lb ? 1 : (a.id < b.id ? -1 : 1));
+        });
+        return candidates;
+    };
 
-            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
-                if (n.properties && n.properties.length > 0) {
-                    let propertiesLength = n.properties.length;
-                    for (let i = 0; i < propertiesLength; ++i) {
-                        let property = n.properties[i];
-                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            let ref = property.ref;
-                            if (!props[ref]) {
-                                props[ref] = new Set();
-                            }
-                            props[ref].add(property.value);
-                        }
+    // Decides whether a property should REPLACE the node names as the
+    // displayed tip label, and which one. Database exports often name their
+    // tips with identifiers (PATRIC.10334.249.FJ478159..., 11320.305060)
+    // while carrying the readable name in a property such as
+    // BVBRC:genome_name. All of the following must hold, or the answer is
+    // null and the names stand:
+    //
+    //   - at least 80% of the named external nodes have identifier-like
+    //     names (no spaces, at least one digit) -- readable names are never
+    //     overridden;
+    //   - the property's local name ends in "name" (genome_name,
+    //     sample_name, ...): only fields that say they are names qualify;
+    //   - it covers at least 90% of the external nodes, is mostly distinct
+    //     (>= 50%), and is mostly wordy (>= 50% of values contain a space)
+    //     -- which is what separates genome_name from strain codes.
+    //
+    // Of several qualifiers, the best-covered wins, ties alphabetically.
+    forester.nodeLabelProperty = function (tree) {
+        let total = 0;
+        let named = 0;
+        let idLike = 0;
+        let refs = {};   // ref -> {covered, values:Set, wordy}
+        forester.preOrderTraversalAll(tree, function (n) {
+            if (n.children || n._children) {
+                return;
+            }
+            total++;
+            if (n.name && String(n.name).trim().length > 0) {
+                named++;
+                let name = String(n.name).trim();
+                if (!/\s/.test(name) && /\d/.test(name)) {
+                    idLike++;
+                }
+            }
+            if (n.properties) {
+                let seen = {};
+                for (let i = 0; i < n.properties.length; ++i) {
+                    let p = n.properties[i];
+                    if (!p.ref || p.applies_to !== 'node' || seen[p.ref]
+                        || p.ref.indexOf(VIS_EXCLUDED_REF_PREFIX) === 0) {
+                        continue;
+                    }
+                    let local = p.ref.indexOf(':') >= 0 ? p.ref.substring(p.ref.indexOf(':') + 1) : p.ref;
+                    if (!/name$/i.test(local)) {
+                        continue;
+                    }
+                    let v = (p.value === undefined || p.value === null) ? '' : String(p.value).trim();
+                    if (v.length === 0) {
+                        continue;
+                    }
+                    seen[p.ref] = true;
+                    if (!refs[p.ref]) {
+                        refs[p.ref] = {covered: 0, values: new Set(), wordy: 0};
+                    }
+                    refs[p.ref].covered++;
+                    refs[p.ref].values.add(v);
+                    if (v.indexOf(' ') >= 0) {
+                        refs[p.ref].wordy++;
                     }
                 }
             }
         });
-        return props;
+        if (named === 0 || idLike * 10 < named * 8) {
+            return null;
+        }
+        let best = null;
+        Object.keys(refs).sort().forEach(function (ref) {
+            let r = refs[ref];
+            if (r.covered * 10 < total * 9) {
+                return;
+            }
+            if (r.values.size * 2 < r.covered) {
+                return;
+            }
+            if (r.wordy * 2 < r.covered) {
+                return;
+            }
+            if (!best || r.covered > refs[best].covered) {
+                best = ref;
+            }
+        });
+        return best;
     };
 
+    // The desktop's reserved "style:" namespace, read back as the rendering
+    // instruction it is (NodeVisualData on the desktop): per-node font colour,
+    // node colour, node shape, font size and font style. The rest of the
+    // vocabulary (font name, node_size, node_transparency, node_fill_type) is
+    // not honoured by this viewer yet. Returns null when the node carries
+    // none of the five.
+    forester.nodeVisualStyle = function (node) {
+        if (!node.properties) {
+            return null;
+        }
+        let style = null;
+        function put(key, value) {
+            if (style === null) {
+                style = {};
+            }
+            style[key] = value;
+        }
+        for (let i = 0; i < node.properties.length; ++i) {
+            let p = node.properties[i];
+            if (!p.ref || p.applies_to !== 'node' || p.value === undefined || p.value === null) {
+                continue;
+            }
+            let v = String(p.value).trim();
+            if (v.length === 0) {
+                continue;
+            }
+            if (p.ref === 'style:font_color') {
+                put('fontColor', v);
+            } else if (p.ref === 'style:node_color') {
+                put('nodeColor', v);
+            } else if (p.ref === 'style:node_shape') {
+                // the desktop's shape names; rectangle renders as our square
+                if (v === 'rectangle') {
+                    put('shape', 'square');
+                } else if (v === 'circle' || v === 'diamond') {
+                    put('shape', v);
+                }
+            } else if (p.ref === 'style:font_size') {
+                let n = Number(v);
+                if (Number.isFinite(n) && n > 0) {
+                    put('fontSize', Math.min(48, Math.max(4, n)));
+                }
+            } else if (p.ref === 'style:font_style') {
+                if (v === 'italic' || v === 'bold' || v === 'bold_italic' || v === 'plain') {
+                    put('fontStyle', v);
+                }
+            }
+        }
+        return style;
+    };
 
-    /**
-     *
-     * Special method for IRD database.
-     * Returns true if at least one 'ird:Host' property with 'Avian' found
-     *
-     * @param phy
-     * @param targetValue
-     * @param fromRef
-     * @param toRef
-     * @returns {boolean}
-     */
-    forester.splitProperty = function (phy, targetValue, fromRef, toRef) {
-        let found = false;
-        let targetValue_ = targetValue + ' ';
-        forester.preOrderTraversalAll(phy, function (n) {
-            if (n.properties && n.properties.length > 0) {
-                let propertiesLength = n.properties.length;
-                for (let i = 0; i < propertiesLength; ++i) {
-                    let property = n.properties[i];
-                    if (property.ref === fromRef && property.value) {
-                        let newValue = '';
-                        if (property.value.startsWith(targetValue_)) {
-                            newValue = targetValue;
-                            found = true;
-                        } else {
-                            newValue = property.value;
-                        }
-                        let newproperty = {};
-                        newproperty.ref = toRef;
-                        newproperty.value = newValue;
-                        newproperty.datatype = 'xsd:string';
-                        newproperty.applies_to = 'node';
-                        n.properties.push(newproperty);
-                    }
+    // The boring part of every tip name. When the displayed names all share
+    // a long prefix ("Influenza A virus ..."), a shortener that keeps the
+    // first characters keeps exactly the characters that carry no
+    // information. This returns the longest common prefix of the displayed
+    // external names -- the label property's value where one is in effect,
+    // the node name otherwise -- cut back to the last separator so no word
+    // is split, and only when it is long enough to matter (>= 6 characters).
+    // The Short Names rendering strips it before truncating, so what
+    // survives is the part that tells the tips apart. The comparison is
+    // case-insensitive -- "Influenza A virus" and "Influenza A Virus" are
+    // the same boring prefix -- so callers must strip by LENGTH, comparing
+    // case-insensitively, not by exact match.
+    forester.commonNamePrefix = function (tree, labelProperty) {
+        let names = [];
+        let slot = labelProperty ? {kind: 'property', ref: labelProperty} : null;
+        forester.preOrderTraversalAll(tree, function (n) {
+            if (n.children || n._children) {
+                return;
+            }
+            let name = slot ? forester.visualizationNodeValue(n, slot) : null;
+            if (name === null && n.name !== undefined && n.name !== null) {
+                let s = String(n.name).trim();
+                if (s.length > 0) {
+                    name = s;
                 }
             }
+            if (name !== null) {
+                names.push(name);
+            }
         });
-        return found;
+        if (names.length < 2) {
+            return '';
+        }
+        let prefix = names[0];
+        for (let k = 1; k < names.length && prefix.length > 0; ++k) {
+            let a = prefix.toLowerCase();
+            let b = names[k].toLowerCase();
+            let max = Math.min(a.length, b.length);
+            let i = 0;
+            while (i < max && a.charCodeAt(i) === b.charCodeAt(i)) {
+                ++i;
+            }
+            if (i < prefix.length) {
+                prefix = prefix.substring(0, i);
+            }
+        }
+        if (prefix.length === 0) {
+            return '';
+        }
+        // Trim back to the last separator ONLY when the prefix actually
+        // splits a word -- "ABC_ho" against "ABC_house"/"ABC_horse" does,
+        // "Influenza A virus" against "...virus A/x" and "...virus(A/y)"
+        // does not, whatever character each name continues with.
+        let alnum = /[A-Za-z0-9]/;
+        let splitsWord = alnum.test(prefix.charAt(prefix.length - 1))
+            && names.some(function (name) {
+                return name.length > prefix.length && alnum.test(name.charAt(prefix.length));
+            });
+        if (splitsWord) {
+            let cut = -1;
+            for (let i = prefix.length - 1; i >= 0; --i) {
+                if (' /|_.-:'.indexOf(prefix.charAt(i)) >= 0) {
+                    cut = i;
+                    break;
+                }
+            }
+            prefix = cut >= 0 ? prefix.substring(0, cut + 1) : '';
+        }
+        return prefix.length >= 6 ? prefix : '';
     };
 
-    forester.collectPropertyRefs = function (phy, appliesTo, externalOnly) {
-        let propertyRefs = new Set();
-        forester.preOrderTraversalAll(phy, function (n) {
-
-            if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
-                if (n.properties && n.properties.length > 0) {
-                    let propertiesLength = n.properties.length;
-                    for (let i = 0; i < propertiesLength; ++i) {
-                        let property = n.properties[i];
-                        if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            propertyRefs.add(property.ref);
+    // Reads a node's value for one candidate, exactly as the classifier read
+    // it when it built the candidate -- the two must never drift, or a node
+    // could carry a value that maps to no colour. Returns the trimmed value,
+    // or null when the node has none (the node then keeps the default look).
+    // Multi-valued refs never become candidates, so "the first value" is
+    // "the only value".
+    forester.visualizationNodeValue = function (node, candidate) {
+        function clean(v) {
+            if (v === undefined || v === null) {
+                return null;
+            }
+            let s = String(v).trim();
+            return s.length > 0 ? s : null;
+        }
+        if (candidate.kind === 'property') {
+            if (node.properties) {
+                for (let i = 0; i < node.properties.length; ++i) {
+                    let p = node.properties[i];
+                    if (p.ref === candidate.ref && p.applies_to === 'node') {
+                        let v = clean(p.value);
+                        if (v !== null) {
+                            // a classifier-built candidate folds the value the
+                            // same way its groups were built; a bare
+                            // {kind, ref} probe (labels, prefixes) reads raw
+                            if (candidate.canon) {
+                                let display = visDisplayLabel(v, candidate.cut || null);
+                                return candidate.canon[display.toLowerCase()] || display;
+                            }
+                            return v;
                         }
                     }
                 }
             }
-        });
-        return propertyRefs;
+            return null;
+        }
+        let list = candidate.kind === 'taxonomy' ? node.taxonomies : node.sequences;
+        if (!list) {
+            return null;
+        }
+        for (let i = 0; i < VIS_ELEMENT_SLOTS.length; ++i) {
+            if (VIS_ELEMENT_SLOTS[i].id === candidate.id) {
+                for (let j = 0; j < list.length; ++j) {
+                    let v = clean(VIS_ELEMENT_SLOTS[i].get(list[j]));
+                    if (v !== null) {
+                        return v;
+                    }
+                }
+                return null;
+            }
+        }
+        return null;
     };
 
-
-    forester.shortenProperties = function (phy, appliesTo, externalOnly, sourceRef, targetRef) {
+    forester.collectPropertyRefs = function (phy, appliesTo, externalOnly) {
+        let propertyRefs = new Set();
         forester.preOrderTraversalAll(phy, function (n) {
+
             if (!externalOnly || externalOnly !== true || (!n.children && !n._children)) {
                 if (n.properties && n.properties.length > 0) {
                     let propertiesLength = n.properties.length;
                     for (let i = 0; i < propertiesLength; ++i) {
                         let property = n.properties[i];
                         if (property.ref && property.value && property.datatype && property.applies_to && property.applies_to === appliesTo) {
-                            if (property.ref === sourceRef) {
-                                let s = property.value.trim().split(/\s+/);
-                                if (s && s.length > 1) {
-                                    let newProp = {};
-                                    newProp.ref = targetRef;
-                                    if (s.length === 2) {
-                                        newProp.value = s[0];
-                                    } else {
-                                        newProp.value = s[0] + ' ' + s[1];
-                                    }
-                                    newProp.datatype = property.datatype;
-                                    newProp.applies_to = property.applies_to;
-                                    n.properties.push(newProp);
-                                }
-                            }
+                            propertyRefs.add(property.ref);
                         }
                     }
                 }
             }
         });
+        return propertyRefs;
     };
 
     forester.collectBasicTreeProperties = function (tree) {
@@ -877,18 +1309,56 @@
         properties.longestNodeName = 0;
         properties.branchLengths = false;
         properties.confidences = false;
+        // the largest confidence value seen -- how a caller tells a
+        // posterior-probability tree (max <= 1) from a bootstrap tree
+        properties.maxConfidence = 0;
         properties.nodeEvents = false;
+        properties.branchColors = false;
         properties.sequences = false;
         properties.taxonomies = false;
         properties.alignedMolSeqs = true;
         properties.maxMolSeqLength = 0;
         properties.externalNodesCount = 0;
-        properties.molSeqResiduesPerPosition = null;
+        properties.nodeCount = 0;
+        // How many of the tree's branches actually carry a positive length.
+        // Whether a tree is worth drawing to scale is a question about the
+        // majority of its branches, not about whether any branch has a length.
+        properties.branchesWithPositiveLength = 0;
+        // Branches that carry a length AT ALL -- an explicit zero is a real
+        // measurement, not a missing one, so these are counted separately from
+        // the "positive" tally above. Split internal-vs-all because a missing
+        // length means different things in the two places: an unmeasured TIP
+        // still draws correctly (at its parent), while an unmeasured INTERNAL
+        // branch destroys the scale. All four counts exclude the root, which
+        // has no branch above it.
+        properties.branchCount = 0;
+        properties.branchesWithLength = 0;
+        properties.internalBranchCount = 0;
+        properties.internalBranchesWithLength = 0;
         properties.averageBranchLength = 0;
         let bl_counter = 0;
         let bl_sum = 0;
-        let molSeqs = [];
-        forester.preOrderTraversalAll(tree, function (n) {
+        // Counting the super-root would add a node and a branch that do not
+        // exist -- skewing the branch-length fraction the viewer uses to choose
+        // between a phylogram and a cladogram -- and from phyloXML would take
+        // the tree's own name for the longest node name.
+        let rootNode = realRootOf(tree);
+        forester.preOrderTraversalAll(rootNode, function (n) {
+            properties.nodeCount += 1;
+            if (n !== rootNode) {
+                let internal = !!(n.children || n._children);
+                let measured = typeof n.branch_length === 'number' && isFinite(n.branch_length);
+                properties.branchCount += 1;
+                if (measured) {
+                    properties.branchesWithLength += 1;
+                }
+                if (internal) {
+                    properties.internalBranchCount += 1;
+                    if (measured) {
+                        properties.internalBranchesWithLength += 1;
+                    }
+                }
+            }
             if (n.name && n.name.length > 0) {
                 properties.nodeNames = true;
                 if (n.name.length > properties.longestNodeName) {
@@ -909,6 +1379,9 @@
             if (n.events) {
                 properties.nodeEvents = true;
             }
+            if (n.color) {
+                properties.branchColors = true;
+            }
             if (n.sequences && n.sequences.length > 0) {
                 properties.sequences = true;
 
@@ -922,8 +1395,6 @@
                         }
                         if (!s.mol_seq.is_aligned) {
                             properties.alignedMolSeqs = false;
-                        } else {
-                            molSeqs.push(s.mol_seq.value);
                         }
                     }
                 }
@@ -936,6 +1407,12 @@
             }
             if (n.confidences && n.confidences.length > 0) {
                 properties.confidences = true;
+                for (let ci = 0; ci < n.confidences.length; ++ci) {
+                    let cv = n.confidences[ci].value;
+                    if (typeof cv === 'number' && isFinite(cv) && cv > properties.maxConfidence) {
+                        properties.maxConfidence = cv;
+                    }
+                }
             }
             if (n.properties && n.properties.length > 0) {
                 let l = n.properties.length;
@@ -948,29 +1425,7 @@
 
         });
 
-        if (properties.alignedMolSeqs) {
-            properties.molSeqResiduesPerPosition = [];
-            for (let p = 0, maxLen = properties.maxMolSeqLength; p < maxLen; ++p) {
-                let mySet = new Set();
-                for (let i = 0, seqsLen = molSeqs.length; i < seqsLen; ++i) {
-                    let molSeq = molSeqs[i];
-                    let c = molSeq[p];
-                    if (c) {
-                        c = c.toUpperCase();
-                        mySet.add(c);
-                        if (!MSA_RESIDUE_SORT_MAP.has(c)) {
-                            throw ("Unknown MSA residue '" + c + "'");
-                        }
-                    }
-
-                }
-                let myArray = forester.setToArray(mySet);
-                myArray.sort(function (a, b) {
-                    return MSA_RESIDUE_SORT_MAP.get(a) - MSA_RESIDUE_SORT_MAP.get(b);
-                });
-                properties.molSeqResiduesPerPosition.push(myArray);
-            }
-        }
+        properties.branchesWithPositiveLength = bl_counter;
 
         if (bl_counter > 0) {
             properties.averageBranchLength = bl_sum / bl_counter;
@@ -1016,23 +1471,52 @@
         return nodes;
     };
 
-    /**
-     * Returns true if at least one of the child nodes
-     * of node is collapsed.
-     *
-     * @param node - A node.
-     * @returns {boolean} - true if at least one of the child nodes is
-     * collapsed
-     */
-    forester.isHasCollapsedNodes = function (node) {
-        let collapsed = false;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n._children) {
-                collapsed = true;
-
+    // Ladderize: at every node, order the VISIBLE children (n.children; a
+    // collapsed node's hidden _children are left untouched) by clade size --
+    // largest first when largestFirst, smallest first when not. Works at ANY
+    // child count, not just 2, so a polytomy (common on a phylodynamic tree,
+    // e.g. an Auspice build, where every internal node may carry 3+ children)
+    // is sorted exactly like a bifurcation. The sort is STABLE (ties keep
+    // their existing relative order), so a node that already reads correctly
+    // is never needlessly disturbed. Mutates the tree in place; returns
+    // whether anything actually changed.
+    forester.ladderize = function (node, largestFirst) {
+        let changed = false;
+        ord(node);
+        return changed;
+
+        function ord(n) {
+            if (!n.children) {
+                return;
             }
-        });
-        return collapsed;
+            let c = n.children;
+            let l = c.length;
+            if (l >= 2) {
+                let counts = c.map(function (child) {
+                    return forester.calcSumOfAllExternalDescendants(child);
+                });
+                let order = c.map(function (child, i) {
+                    return i;
+                });
+                order.sort(function (i, j) {
+                    if (counts[i] === counts[j]) {
+                        return i - j;
+                    }
+                    return largestFirst ? (counts[j] - counts[i]) : (counts[i] - counts[j]);
+                });
+                if (order.some(function (idx, i) {
+                    return idx !== i;
+                })) {
+                    changed = true;
+                    n.children = order.map(function (idx) {
+                        return c[idx];
+                    });
+                }
+            }
+            for (let i = 0; i < n.children.length; ++i) {
+                ord(n.children[i]);
+            }
+        }
     };
 
     forester.getAllExternalNodes = function (node) {
@@ -1126,77 +1610,349 @@
         });
     };
 
-
-    forester.collapseToBranchLength = function (root, branchLength) {
-        if (root.children && root.children.length === 1) {
-            collapseToBranchLengthHelper(root.children[0], branchLength);
+    forester.collapse = function (node) {
+        if (node.children) {
+            node._children = node.children;
+            node.children = null;
         }
+    };
 
-        function collapseToBranchLengthHelper(n, branchLength) {
-            if (!(n.children || n._children)) {
-                return;
-            }
-
-            if (!n.max) {
-                n.max = forester.calcMaxBranchLength(n);
-            }
-            let max = n.max;
-            if (max < branchLength) {
-                forester.collapse(n);
-            } else {
-                forester.unCollapse(n);
-                for (let i = n.children.length - 1; i >= 0; i--) {
-                    collapseToBranchLengthHelper(n.children[i], branchLength);
-                }
-            }
+    forester.unCollapse = function (node) {
+        if (node._children) {
+            node.children = node._children;
+            node._children = null;
         }
     };
 
-    forester.collapseToDepth = function (root, depth) {
-        if (root.children && root.children.length === 1) {
-            collapseToDepthHelper(root.children[0], 0, depth);
+    /**
+     * To parse a New Hampshire (Newick) formatted tree.
+     *
+     * @param nhStr - A New Hampshire (Newick) formatted string.
+     * @param confidenceValuesInBrackets - Set to true if confidence values are in brackets (default: true)
+     *                                     Format is: name:distance[confidence]
+     *                                     Example: "bcl2:0.000393[95]"
+     * @param confidenceValuesAsInternalNames - Set to true if confidence values are represented by internal names (default: false).
+     * @returns {{}} - A phylogenetic tree object.
+     */
+    // ---------------------------------------------------------------
+    // Extended Newick annotations: BEAST-style [&key=value,...] and
+    // NHX [&&NHX:tag=value:...]
+    // ---------------------------------------------------------------
+    //
+    // ALWAYS parsed (the desktop keeps this behind a
+    // setParseBeastStyleExtendedTags option; here the blobs were simply
+    // discarded before, so ingesting them can regress nothing). Ported from
+    // the desktop's BeastAnnotationParser + the NHXParser tag loop.
+
+    // Pre-tokenization pass: pull every [&...] annotation out of the Newick
+    // string and leave a [@N] marker in its place -- the blob's commas,
+    // colons and quotes must never reach the Newick tokenizer. A bracket NOT
+    // starting with '&' (a [95] confidence) is left untouched, as is any
+    // bracket inside a quoted label. Quotes and nested brackets inside an
+    // annotation are honoured when finding its end.
+    function extractBracketAnnotations(str) {
+        if (str.indexOf('[') < 0) {
+            return {text: str, blobs: []};
+        }
+        let out = '';
+        let blobs = [];
+        let inSq = false;
+        let inDq = false;
+        for (let i = 0; i < str.length; ++i) {
+            let c = str.charAt(i);
+            if (inSq || inDq) {
+                out += c;
+                if ((inSq && c === "'") || (inDq && c === '"')) {
+                    inSq = false;
+                    inDq = false;
+                }
+            } else if (c === "'") {
+                inSq = true;
+                out += c;
+            } else if (c === '"') {
+                inDq = true;
+                out += c;
+            } else if (c === '[') {
+                let j = i + 1;
+                let depth = 1;
+                let q = null;
+                while (j < str.length && depth > 0) {
+                    let cj = str.charAt(j);
+                    if (q) {
+                        if (cj === q) {
+                            q = null;
+                        }
+                    } else if (cj === "'" || cj === '"') {
+                        q = cj;
+                    } else if (cj === '[') {
+                        ++depth;
+                    } else if (cj === ']') {
+                        --depth;
+                    }
+                    if (depth > 0) {
+                        ++j;
+                    }
+                }
+                let content = str.substring(i + 1, j);
+                if (/^\s*&/.test(content)) {
+                    out += '[@' + blobs.length + ']';
+                    blobs.push(content.trim());
+                } else {
+                    out += str.substring(i, Math.min(j + 1, str.length));
+                }
+                i = j;
+            } else {
+                out += c;
+            }
         }
+        return {text: out, blobs: blobs};
+    }
 
-        function collapseToDepthHelper(n, d, depth) {
-            if (!n.children && !n._children) {
+    function pushConfidence(node, value, type, stddev) {
+        if (!node.confidences) {
+            node.confidences = [];
+        }
+        let c = {type: type, value: value};
+        if (stddev !== undefined && stddev !== null) {
+            c.stddev = stddev;
+        }
+        node.confidences.push(c);
+    }
+
+    function nodeTaxonomy0(node) {
+        if (!node.taxonomies) {
+            node.taxonomies = [{}];
+        }
+        return node.taxonomies[0];
+    }
+
+    function nodeSequence0(node) {
+        if (!node.sequences) {
+            node.sequences = [{}];
+        }
+        return node.sequences[0];
+    }
+
+    // Split on TOP-LEVEL commas only: a comma inside {...}/[...] sets or
+    // inside quotes is data, not a separator (height_95%_HPD={1.4,1.5} must
+    // stay one token).
+    function splitTopLevelCommas(s) {
+        let out = [];
+        let depth = 0;
+        let q = null;
+        let cur = '';
+        for (let i = 0; i < s.length; ++i) {
+            let c = s.charAt(i);
+            if (q) {
+                if (c === q) {
+                    q = null;
+                }
+                cur += c;
+            } else if (c === "'" || c === '"') {
+                q = c;
+                cur += c;
+            } else if (c === '{' || c === '[') {
+                ++depth;
+                cur += c;
+            } else if (c === '}' || c === ']') {
+                if (depth > 0) {
+                    --depth;
+                }
+                cur += c;
+            } else if (c === ',' && depth === 0) {
+                out.push(cur);
+                cur = '';
+            } else {
+                cur += c;
+            }
+        }
+        if (cur.length > 0) {
+            out.push(cur);
+        }
+        return out;
+    }
+
+    function parseBeastNumber(v) {
+        let d = parseFloat(v);
+        return (isFinite(d) && isFinite(Number(v))) ? d : null;
+    }
+
+    // A two-value BEAST set {lo,hi} (or [lo,hi]) as [lo,hi] numbers, or null.
+    function parseBeastInterval(v) {
+        let s = v.trim();
+        if (s.length < 3 || (s.charAt(0) !== '{' && s.charAt(0) !== '[')) {
+            return null;
+        }
+        let parts = splitTopLevelCommas(s.substring(1, s.length - 1));
+        if (parts.length !== 2) {
+            return null;
+        }
+        let lo = parseBeastNumber(parts[0].trim());
+        let hi = parseBeastNumber(parts[1].trim());
+        return (lo !== null && hi !== null) ? [lo, hi] : null;
+    }
+
+    function stripValueQuotes(v) {
+        if (v.length >= 2
+            && ((v.charAt(0) === '"' && v.charAt(v.length - 1) === '"')
+                || (v.charAt(0) === "'" && v.charAt(v.length - 1) === "'"))) {
+            return v.substring(1, v.length - 1);
+        }
+        return v;
+    }
+
+    // A property-ref-safe rendering of a BEAST key: keep letters/digits,
+    // collapse every other run to one underscore, drop a trailing one
+    // (rate_95%_HPD -> a clean beast:rate_95_HPD ref).
+    function beastRefKey(key) {
+        return key.replace(/[^A-Za-z0-9]+/g, '_').replace(/_$/, '');
+    }
+
+    // A BEAST / BEAST X / TreeAnnotator / FigTree / MrBayes [&...] blob onto
+    // one node, each field mapped to the phyloXML structure the existing
+    // display features consume:
+    //  - posterior -> a confidence of type "posterior"; MrBayes prob (+
+    //    prob_stddev) -> "posterior probability"; bootstrap -> "bootstrap";
+    //  - node age height/height_mean/height_median + height_95%_HPD (or
+    //    height_range) + date -> node.date value/min/max/desc (the node-age
+    //    HPD bars draw the interval);
+    //  - FigTree !color=#rrggbb -> the branch color;
+    //  - every other field (rate, length_*, traits, location, ...) -> a
+    //    beast:<key> node property (numeric -> xsd:decimal, so Color-by
+    //    picks it up).
+    // The branch length lives on the Newick ":length" and is left untouched.
+    // A malformed field is skipped, never aborting the parse.
+    function applyBeastAnnotations(node, blob) {
+        let heightMedian = null;
+        let heightMean = null;
+        let height = null;
+        let hpd = null;
+        let range = null;
+        let dateDesc = null;
+        let prob = null;
+        let probSd = null;
+        splitTopLevelCommas(blob).forEach(function (token) {
+            let eq = token.indexOf('=');
+            if (eq <= 0) {
                 return;
             }
-            if (d >= depth) {
-                forester.collapse(n);
-            } else {
-                forester.unCollapse(n);
-                ++d;
-                for (let i = n.children.length - 1; i >= 0; i--) {
-                    collapseToDepthHelper(n.children[i], d, depth);
+            let key = token.substring(0, eq).trim();
+            let value = stripValueQuotes(token.substring(eq + 1).trim());
+            if (key.length === 0 || value.length === 0) {
+                return;
+            }
+            let kl = key.toLowerCase();
+            if (kl === 'posterior') {
+                let d = parseBeastNumber(value);
+                if (d !== null) {
+                    pushConfidence(node, d, 'posterior');
                 }
+            } else if (kl === 'prob') {
+                prob = parseBeastNumber(value);
+            } else if (kl === 'prob_stddev') {
+                probSd = parseBeastNumber(value);
+            } else if (kl === 'bootstrap') {
+                let b = parseBeastNumber(value);
+                if (b !== null) {
+                    pushConfidence(node, b, 'bootstrap');
+                }
+            } else if ((kl === '!color' || kl === '!colour')
+                && /^#[0-9a-f]{6}$/i.test(value)) {
+                node.color = {
+                    red: parseInt(value.substring(1, 3), 16),
+                    green: parseInt(value.substring(3, 5), 16),
+                    blue: parseInt(value.substring(5, 7), 16)
+                };
+            } else if (kl === 'height_median') {
+                heightMedian = value;
+            } else if (kl === 'height_mean') {
+                heightMean = value;
+            } else if (kl === 'height') {
+                height = value;
+            } else if (kl === 'height_95%_hpd') {
+                hpd = parseBeastInterval(value);
+            } else if (kl === 'height_range') {
+                range = parseBeastInterval(value);
+            } else if (kl === 'date') {
+                dateDesc = value;
+            } else {
+                addNodeProperty(node, 'beast:' + beastRefKey(key), value);
             }
+        });
+        if (prob !== null) {
+            pushConfidence(node, prob, 'posterior probability', probSd);
         }
-    };
-
-    forester.collapse = function (node) {
-        if (node.children) {
-            node._children = node.children;
-            node.children = null;
+        // age preference: median, then mean, then height -- and each piece
+        // parsed independently, so an unparseable point value never discards
+        // a valid {lo,hi} interval
+        let v = heightMedian !== null ? heightMedian
+            : (heightMean !== null ? heightMean : height);
+        let dv = (v !== null) ? parseBeastNumber(v) : null;
+        let interval = hpd || range;
+        if (dv === null && !interval && dateDesc === null) {
+            return;
         }
-    };
+        let date = {};
+        if (dv !== null) {
+            date.value = dv;
+        }
+        if (interval) {
+            date.minimum = interval[0];
+            date.maximum = interval[1];
+        }
+        if (dateDesc !== null) {
+            date.desc = dateDesc;
+        }
+        node.date = date;
+    }
 
-    forester.unCollapse = function (node) {
-        if (node._children) {
-            node.children = node._children;
-            node._children = null;
+    // The classic NHX tag set, as the desktop maps it: S= taxonomy
+    // scientific name, T= taxonomy id, B= support confidence, D= a
+    // duplication (Y/T) / speciation (N/F) / undecided (?) event, GN=
+    // sequence name, AC= sequence accession, C= an nh:comment property.
+    // Unknown tags (and DS= domain structures) are ignored.
+    function applyNhxTags(node, content) {
+        content.split(':').forEach(function (tag) {
+            let t = tag.trim();
+            if (t.length < 3) {
+                return;
+            }
+            if (t.startsWith('S=')) {
+                nodeTaxonomy0(node).scientific_name = t.substring(2);
+            } else if (t.startsWith('T=')) {
+                nodeTaxonomy0(node).id = {value: t.substring(2)};
+            } else if (t.startsWith('B=')) {
+                let b = parseBeastNumber(t.substring(2));
+                if (b !== null) {
+                    pushConfidence(node, b, 'bootstrap');
+                }
+            } else if (t.startsWith('D=')) {
+                let c = t.charAt(2);
+                if (c === 'Y' || c === 'T') {
+                    node.events = {duplications: 1};
+                } else if (c === 'N' || c === 'F') {
+                    node.events = {speciations: 1};
+                } else if (c === '?') {
+                    node.events = {type: 'speciation_or_duplication'};
+                }
+            } else if (t.startsWith('GN=')) {
+                nodeSequence0(node).name = t.substring(3);
+            } else if (t.startsWith('AC=')) {
+                nodeSequence0(node).accession = {value: t.substring(3), source: '?'};
+            } else if (t.startsWith('C=')) {
+                addNodeProperty(node, 'nh:comment', t.substring(2));
+            }
+        });
+    }
+
+    function applyExtendedAnnotations(node, blob) {
+        if (/^&&NHX:/i.test(blob)) {
+            applyNhxTags(node, blob.substring(6));
+        } else {
+            applyBeastAnnotations(node, blob.replace(/^&/, ''));
         }
-    };
+    }
 
-    /**
-     * To parse a New Hampshire (Newick) formatted tree.
-     *
-     * @param nhStr - A New Hampshire (Newick) formatted string.
-     * @param confidenceValuesInBrackets - Set to true if confidence values are in brackets (default: true)
-     *                                     Format is: name:distance[confidence]
-     *                                     Example: "bcl2:0.000393[95]"
-     * @param confidenceValuesAsInternalNames - Set to true if confidence values are represented by internal names (default: false).
-     * @returns {{}} - A phylogenetic tree object.
-     */
     forester.parseNewHampshire = function (nhStr, confidenceValuesInBrackets, confidenceValuesAsInternalNames) {
 
         let NH_FORMAT_ERR_OPEN_PARENS = NH_FORMAT_ERR + 'likely cause: number of open parentheses is larger than number of close parentheses';
@@ -1208,14 +1964,22 @@
         if (confidenceValuesAsInternalNames === undefined) {
             confidenceValuesAsInternalNames = false;
         }
-        if ((confidenceValuesInBrackets === true) && (confidenceValuesAsInternalNames === true)) {
-            throw ("confidence values cannot be both in brackets and as internal node names");
-        }
+        // The two options used to be mutually exclusive and throwing. They are
+        // not: brackets are consumed by the tokenizer, bare labels are handled
+        // afterwards, so a file mixing the two dialects is read correctly with
+        // both on. forester-Java never had this guard, so it was never part of
+        // the shared contract -- and throwing on a combination a user
+        // plausibly wants is what forced callers into workarounds.
 
         let ancs = [];
         let x = {};
 
-        let sss = nhStr.replace(/\[\s*&.+?\]/g, '');
+        // [&...] annotation blobs (BEAST-style key=value, NHX) are pulled
+        // out BEFORE tokenizing -- their commas/colons/quotes are data --
+        // and re-attached to their node via the [@N] markers below
+        let extracted = extractBracketAnnotations(nhStr);
+        let sss = extracted.text;
+        let annotations = extracted.blobs;
 
         let ss = sss.split(/(;|\(|\)|,|:|"|')/);
         let ssl = ss.length;
@@ -1271,10 +2035,24 @@
                     } else if (element === ')') {
                         x = ancs.pop();
                     } else if (element === ':') {
+                        // the separator before a branch length: the length itself
+                        // is read by the branch below, so there is nothing to do here
                     } else {
                         let e = ss[i - 1];
                         if (e) {
                             e = e.trim();
+                            // re-attach any annotation blobs riding on this
+                            // element (name, branch length, or standalone) to
+                            // the current node, and drop the markers
+                            if (annotations.length > 0 && element.indexOf('[@') > -1) {
+                                element = element.replace(/\[@(\d+)\]/g, function (m, k) {
+                                    let blob = annotations[+k];
+                                    if (blob !== undefined) {
+                                        applyExtendedAnnotations(x, blob);
+                                    }
+                                    return '';
+                                });
+                            }
                             if ((e === ')') || (e === '(') || (e === ',')) {
                                 if (element && element.length > 0) {
                                     if (element.charAt(element.length - 1) === "]") {
@@ -1410,221 +2188,762 @@
         }
     };
 
-    forester.isNumber = function (v) {
-        if (v === undefined || v === null) {
-            return false;
-        }
-        if (v != v) {
-            // This can only be true if the v is NaN
-            return false;
+    // Parses a Nexus-formatted string and returns an ARRAY of tree objects,
+    // each in the same shape parseNewHampshire produces (a Nexus file can
+    // hold any number of trees). Ported from the desktop's
+    // NexusPhylogeniesParser: reads TAXLABELS, the TREES block (TRANSLATE
+    // tables, TREE/UTREE statements, [&R]/[&U] rootedness, tree names and
+    // titles) and CHARACTERS/DATA blocks -- a protein/dna/rna MATRIX
+    // (sequential or interleaved, MATCHCHAR resolved, quoted labels,
+    // comments stripped) becomes per-tip aligned molecular sequences in the
+    // phyloXML shape (sequences[i].mol_seq.{is_aligned,value}), so a tree
+    // read from Nexus shows its alignment track exactly like one read from
+    // phyloXML. The two confidence options are handed through to
+    // parseNewHampshire for each tree statement.
+    forester.parseNexus = function (nexStr, confidenceValuesInBrackets, confidenceValuesAsInternalNames) {
+        const NEXUS_FORMAT_ERR = 'Nexus format error: ';
+        const TITLE_RE = /^title.?\s+([^;]+)/i;
+        const TREE_NAME_RE = /^\s*.?tree\s+(.+?)\s*=/i;
+        const ROOTEDNESS_RE = /=\s*\[&([RU])\]/i;
+        const TRANSLATE_PAIR_RE = /([0-9A-Za-z]+)\s+(.+)/;
+        const RESIDUES_RE = /^[A-Za-z\-_*?.]+$/;
+        const DATATYPE_RE = /datatype\s*=\s*([a-z]+)/;
+        const MATCHCHAR_RE = /matchchar\s*=\s*['"]?(\S)/;
+
+        let trees = [];
+        let taxlabels = [];
+        // null-prototype maps: a taxon named "__proto__" must stay data
+        let translateMap = Object.create(null);
+        let seqs = Object.create(null);
+        let translateBuf = '';
+        let nh = '';
+        let name = '';
+        let title = '';
+        let inTreesBlock = false;
+        let inTaxalabels = false;
+        let inTranslate = false;
+        let inTree = false;
+        let inDataBlock = false;
+        let inMatrix = false;
+        let inDataComment = false;
+        let datatype = null;
+        let rootedInfoPresent = false;
+        let isRooted = false;
+        let matchchar = null;
+        let matrixReferenceId = null;
+
+        // Nexus treats '_' and ' ' as equivalent, labels may be quoted, and a
+        // matrix often capitalizes taxon names differently from the tree -- so
+        // a matrix row joins its tree tip through this canonical key.
+        function joinKey(s) {
+            return s.replace(/_/g, ' ').replace(/['"]+/g, '').trim().toLowerCase();
         }
-        return true;
-    };
-
-    forester.getOneDistinctTaxonomy = function (node) {
-        let id = null;
-        let code = null;
-        let sn = null;
-        let cn = null;
-        let result = true;
-        let sawTax = false;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.taxonomies && n.taxonomies.length === 1) {
-                let tax = n.taxonomies[0];
-                if (tax.code && tax.code.length > 0) {
-                    sawTax = true;
-                    if (code === null) {
-                        code = tax.code;
-                    } else if (code !== tax.code) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.scientific_name && tax.scientific_name.length > 0) {
-                    sawTax = true;
-                    if (sn === null) {
-                        sn = tax.scientific_name;
-                    } else if (sn !== tax.scientific_name) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.common_name && tax.common_name.length > 0) {
-                    sawTax = true;
-                    if (cn === null) {
-                        cn = tax.common_name;
-                    } else if (cn !== tax.common_name) {
-                        result = false;
-                        return;
-                    }
-                }
-                if (tax.id && tax.id.value && tax.id.value.length > 0) {
-                    sawTax = true;
-                    let myid;
-                    if (tax.id.provider && tax.id.provider.length > 0) {
-                        myid = tax.id.provider + ':' + tax.id.value;
-                    } else {
-                        myid = tax.id.value;
-                    }
-                    if (id === null) {
-                        id = myid;
-                    } else if (id !== myid) {
-                        result = false;
 
+        // Strip Nexus [ ... ] comments, tracking an OPEN comment across lines
+        // so a multi-line comment inside the matrix cannot leak prose as a
+        // spurious taxon row. Called only inside the data block -- the trees
+        // block keeps [&R]/[&...], which are semantic there.
+        function stripDataComments(s) {
+            if (!inDataComment && s.indexOf('[') < 0) {
+                return s;
+            }
+            let out = '';
+            for (let i = 0; i < s.length; ++i) {
+                let c = s.charAt(i);
+                if (inDataComment) {
+                    if (c === ']') {
+                        inDataComment = false;
                     }
+                } else if (c === '[') {
+                    inDataComment = true;
+                } else {
+                    out += c;
                 }
-            } else if (!n.children && !n._children) {
-                // If an external node lacks taxonomy, return false.
-                result = false;
             }
-        });
-        if (!sawTax) {
-            return null;
+            return out.trim();
         }
-        if (result === true) {
 
-            if (sn) {
-                return sn;
-            } else if (code) {
-                return code;
-            } else if (cn) {
-                return cn;
-            } else if (id) {
-                return id;
+        function setTranslatePairs(buf) {
+            let s = buf.trim();
+            if (s.endsWith(';')) {
+                s = s.slice(0, -1).trim();
             }
+            // splitTopLevelCommas, not a plain split: a quoted label may
+            // itself contain a comma ('Korea, Republic of' -- the very case
+            // the Auspice writer quotes against elsewhere in this file)
+            splitTopLevelCommas(s).forEach(function (pair) {
+                let ti = pair.toLowerCase().indexOf('translate');
+                if (ti > -1) {
+                    pair = pair.substring(ti + 9);
+                }
+                if (pair.trim().length === 0) {
+                    return; // a trailing comma before the ';' is tolerated
+                }
+                let m = TRANSLATE_PAIR_RE.exec(pair);
+                if (!m) {
+                    throw new Error(NEXUS_FORMAT_ERR + 'ill-formatted translate table entry: "'
+                        + pair.trim() + '" -- is the Translate sub-command terminated with a ";"?');
+                }
+                let value = m[2].replace(/['"]+/g, '').trim();
+                if (value.endsWith(';')) {
+                    value = value.slice(0, -1);
+                }
+                translateMap[m[1]] = value;
+            });
         }
-        return null;
-    };
 
-    forester.getOneDistinctNodePropertyValue = function (node, propertyRef) {
-        let propValue = null;
-        let result = true;
-        forester.preOrderTraversalAll(node, function (n) {
-            if (n.properties && n.properties.length > 0) {
-                let propertiesLength = n.properties.length;
-                let gotIt = false;
-                for (let i = 0; i < propertiesLength; ++i) {
-                    let property = n.properties[i];
-                    if (property.ref && property.value && (property.applies_to === 'node') && (property.ref === propertyRef) && (property.value.length > 0)) {
-                        if (propValue === null) {
-                            propValue = property.value;
-                        } else if (propValue !== property.value) {
-                            result = false;
-                            return;
-                        }
-                        gotIt = true;
-                    }
+        // One MATRIX row ("taxon residues..."): the id is the first token (a
+        // quoted label may contain spaces), the residues are the rest with all
+        // internal whitespace removed. Only protein/dna/rna matrices become
+        // sequences. In an interleaved matrix each id reappears in a later
+        // block, so a repeated id is CONCATENATED onto its row. MATCHCHAR
+        // (e.g. '.') means "same as the first taxon at this position" and is
+        // resolved against that reference row at the same absolute positions.
+        function addMatrixRow(row) {
+            if (datatype !== 'protein' && datatype !== 'dna' && datatype !== 'rna') {
+                return;
+            }
+            let id;
+            let rest;
+            let c0 = row.charAt(0);
+            if (c0 === "'" || c0 === '"') {
+                let close = row.indexOf(c0, 1);
+                if (close < 1) {
+                    return;
                 }
-                if (!gotIt && !n.children && !n._children) {
-                    // If an external node lacks propertyRef, return false.
-                    result = false;
-
+                id = row.substring(0, close + 1);
+                rest = row.substring(close + 1);
+            } else {
+                let sp = row.indexOf(' ');
+                if (sp < 1) {
+                    return;
                 }
+                id = row.substring(0, sp);
+                rest = row.substring(sp + 1);
+            }
+            let block = rest.replace(/\s+/g, '');
+            if (block.length === 0 || !RESIDUES_RE.test(block)) {
+                return;
+            }
+            if (matchchar && (matrixReferenceId !== null) && (id !== matrixReferenceId)
+                && seqs[matrixReferenceId]) {
+                let ref = seqs[matrixReferenceId].value;
+                let offset = seqs[id] ? seqs[id].value.length : 0;
+                let resolved = '';
+                for (let j = 0; j < block.length; ++j) {
+                    let c = block.charAt(j);
+                    resolved += (c === matchchar && (offset + j) < ref.length)
+                        ? ref.charAt(offset + j) : c;
+                }
+                block = resolved;
+            }
+            seqs[id] = {
+                value: seqs[id] ? (seqs[id].value + block) : block,
+                type: datatype
+            };
+            if (matrixReferenceId === null) {
+                matrixReferenceId = id;
             }
-        });
-        if (propValue === null) {
-            return null;
-        }
-        if (result === true) {
-            return propValue;
-        } else {
-            return null;
         }
-    };
 
-    /**
-     * To be deprecated!
-     *
-     * @param phy
-     * @returns {{}}
-     */
-    forester.moveSimpleCharacteristicsToProperties = function (phy) {
-        let apptype;
-        if (phy.desc) {
-            apptype = 'ird:'
-        } else {
-            apptype = 'vipr:'
+        // A complete tree statement has accumulated in nh: parse it and carry
+        // over the block's translate table / taxlabels / matrix sequences.
+        function finishTree() {
+            if (nh.length === 0) {
+                return;
+            }
+            let phy = forester.parseNewHampshire(nh, confidenceValuesInBrackets, confidenceValuesAsInternalNames);
+            let myname = '';
+            if (title && name) {
+                myname = title.replace(/_/g, ' ').trim() + ' (' + name.trim() + ')';
+            } else if (title) {
+                myname = title.replace(/_/g, ' ').trim();
+            } else if (name) {
+                myname = name.trim();
+            }
+            if (myname) {
+                phy.name = myname;
+            }
+            if (rootedInfoPresent) {
+                phy.rooted = isRooted;
+            }
+            let seqsByKey = Object.create(null);
+            for (let id in seqs) {
+                seqsByKey[joinKey(id)] = seqs[id];
+            }
+            forester.getAllExternalNodes(phy).forEach(function (node) {
+                if (node.name && translateMap[node.name] !== undefined) {
+                    node.name = translateMap[node.name];
+                } else if (taxlabels.length > 0 && node.name && /^\d+$/.test(node.name)) {
+                    let i = parseInt(node.name, 10);
+                    if (i > 0 && i <= taxlabels.length) {
+                        node.name = taxlabels[i - 1].replace(/['"]+/g, '');
+                    }
+                }
+                if (node.name) {
+                    let s = seqsByKey[joinKey(node.name)];
+                    if (s) {
+                        if (!node.sequences) {
+                            node.sequences = [];
+                        }
+                        node.sequences.push({
+                            type: s.type,
+                            mol_seq: {is_aligned: true, value: s.value}
+                        });
+                    }
+                }
+            });
+            trees.push(phy);
+            nh = '';
+            name = '';
+            rootedInfoPresent = false;
+            isRooted = false;
         }
 
-        let HOST = apptype + 'Host';
-        let COUNTRY = apptype + 'Country';
-        let YEAR = apptype + 'Year';
-        let HA = apptype + 'HA';
-        let NA = apptype + 'NA';
-        let NODE = 'node';
-        let STRING = 'xsd:string';
-        let INT = 'xsd:integer';
-
-        forester.preOrderTraversalAll(phy, function (n) {
-            if (n.simple_characteristics) {
-                let sc = n.simple_characteristics;
-                let props;
-                if (sc.country && sc.country.length > 0) {
-                    props = {};
-                    props.ref = COUNTRY;
-                    props.datatype = STRING;
-                    props.applies_to = NODE;
-                    props.value = sc.country;
-                    addProperties(n, props);
-                }
-                if (sc.host && sc.host.length > 0) {
-                    props = {};
-                    props.ref = HOST;
-                    props.datatype = STRING;
-                    props.applies_to = NODE;
-                    props.value = sc.host;
-                    addProperties(n, props);
-                }
-                if (sc.year && sc.year.length > 0) {
-                    props = {};
-                    props.ref = YEAR;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.year);
-                    addProperties(n, props);
-                }
-                if (sc.ha && sc.ha.length > 0) {
-                    props = {};
-                    props.ref = HA;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.ha);
-                    addProperties(n, props);
-                }
-                if (sc.na && sc.na.length > 0) {
-                    props = {};
-                    props.ref = NA;
-                    props.datatype = INT;
-                    props.applies_to = NODE;
-                    props.value = parseInt(sc.na);
-                    addProperties(n, props);
-                }
-                n.simple_characteristics = undefined;
+        let lines = String(nexStr).split(/\r\n|\r|\n/);
+        for (let k = 0; k < lines.length; ++k) {
+            let line = lines[k].trim();
+            if (line.length === 0 || line.charAt(0) === '#' || line.charAt(0) === '>') {
+                continue;
             }
-        });
-
-        function addProperties(n, props) {
-            if (props) {
-                if (!n.properties) {
-                    n.properties = [];
+            line = line.replace(/\s+/g, ' ').replace(/\s+;/g, ';');
+            let lc = line.toLowerCase();
+            if (/^begin\s+trees\b/.test(lc)) {
+                inTreesBlock = true;
+                inTaxalabels = false;
+                inTranslate = false;
+                inDataBlock = false;
+                datatype = null;
+                title = '';
+            } else if (lc.startsWith('taxlabels')) {
+                inTreesBlock = false;
+                inTaxalabels = true;
+                inTranslate = false;
+                inDataBlock = false;
+                datatype = null;
+            } else if (lc.startsWith('translate')) {
+                translateBuf = '';
+                inTaxalabels = false;
+                inTranslate = true;
+                inDataBlock = false;
+                datatype = null;
+            } else if (/^begin\s+(characters|data)\b/.test(lc)) {
+                inTaxalabels = false;
+                inTreesBlock = false;
+                inTranslate = false;
+                inDataBlock = true;
+                inMatrix = false;
+                inDataComment = false;
+                datatype = null;
+                matchchar = null;
+                matrixReferenceId = null;
+                // scope the rows to THIS matrix block, so a later block
+                // cannot cross-contaminate an earlier one
+                seqs = Object.create(null);
+            } else if (inTreesBlock) {
+                if (lc.startsWith('title')) {
+                    let tm = TITLE_RE.exec(line);
+                    if (tm) {
+                        title = tm[1];
+                    }
+                } else if (lc.startsWith('link')) {
+                    // a LINK sub-command (e.g. "LINK TAXA=...") -- ignored
+                } else if (lc.startsWith('end;') || lc.startsWith('endblock')) {
+                    inTreesBlock = false;
+                    inTree = false;
+                    finishTree();
+                } else if (lc.startsWith('tree ') || lc.startsWith('utree ')) {
+                    finishTree(); // a previous statement still pending
+                    inTree = true;
+                    let nm = TREE_NAME_RE.exec(line);
+                    if (nm) {
+                        name = nm[1].replace(/['"]+/g, '');
+                    }
+                    let rm = ROOTEDNESS_RE.exec(line);
+                    if (rm) {
+                        rootedInfoPresent = true;
+                        isRooted = rm[1].toUpperCase() === 'R';
+                    }
+                    // parseNewHampshire handles the remaining [&...] hot
+                    // comments itself: BEAST-style annotations are parsed
+                    // onto the nodes, a leading [&R]/[&U] is dropped
+                    nh = line.substring(line.indexOf('=') + 1).trim();
+                    if (lc.endsWith(';')) {
+                        inTree = false;
+                        finishTree();
+                    }
+                } else if (inTree) {
+                    nh += line;
+                    if (lc.endsWith(';')) {
+                        inTree = false;
+                        finishTree();
+                    }
                 }
-                let alreadyHave = false;
-                let l = n.properties.length;
-                for (let i = 0; i < l; ++i) {
-                    if (n.properties[i].ref === props.ref) {
-                        alreadyHave = true;
-                        break;
+            }
+            if (inTaxalabels) {
+                if (lc.startsWith('end;') || lc.startsWith('endblock')) {
+                    inTaxalabels = false;
+                } else {
+                    // QUOTE-AWARE tokenization: 'Homo sapiens' is ONE label
+                    // (that is what the quotes are for) -- a plain space split
+                    // silently sheared such labels apart and shifted every
+                    // numeric tip onto the wrong name. ';' (unquoted) ends
+                    // the sub-command.
+                    let tok = '';
+                    let q = null;
+                    let push = function () {
+                        if (tok.length > 0 && tok.toLowerCase() !== 'taxlabels') {
+                            taxlabels.push(tok);
+                        }
+                        tok = '';
+                    };
+                    for (let ci = 0; ci < line.length; ++ci) {
+                        let ch = line.charAt(ci);
+                        if (q) {
+                            if (ch === q) {
+                                q = null;
+                            } else {
+                                tok += ch;
+                            }
+                        } else if (ch === "'" || ch === '"') {
+                            q = ch;
+                        } else if (ch === ' ') {
+                            push();
+                        } else if (ch === ';') {
+                            inTaxalabels = false;
+                            push();
+                            break;
+                        } else {
+                            tok += ch;
+                        }
+                    }
+                    push();
+                }
+            }
+            if (inTranslate) {
+                if (lc.startsWith('end;') || lc.startsWith('endblock')) {
+                    inTranslate = false;
+                } else {
+                    translateBuf += ' ' + line;
+                    if (line.endsWith(';')) {
+                        inTranslate = false;
+                        setTranslatePairs(translateBuf);
                     }
                 }
-                if (!alreadyHave) {
-                    n.properties.push(props);
+            }
+            if (inDataBlock) {
+                line = stripDataComments(line);
+                let dlc = line.toLowerCase();
+                if (line.length === 0) {
+                    // comment-only (or now-empty) line
+                } else if (dlc.startsWith('end;') || dlc.startsWith('endblock')) {
+                    inDataBlock = false;
+                    inMatrix = false;
+                    datatype = null;
+                } else if (dlc.startsWith('link ')) {
+                    // ignored; the trailing space keeps a taxon row whose
+                    // name starts with "link" out of this branch
+                } else if (!inMatrix) {
+                    // block header: DIMENSIONS / FORMAT / CHARLABELS / ... --
+                    // read DATATYPE and MATCHCHAR off FORMAT, enter the matrix
+                    // on the MATRIX keyword, ignore the rest (a sub-command
+                    // ending in ';' must NOT be mistaken for the block's end)
+                    let dm = DATATYPE_RE.exec(dlc);
+                    if (dm) {
+                        datatype = dm[1];
+                    }
+                    let mm = MATCHCHAR_RE.exec(dlc);
+                    if (mm) {
+                        matchchar = mm[1];
+                    }
+                    if (dlc === 'matrix' || dlc.startsWith('matrix ')) {
+                        inMatrix = true;
+                        let after = line.substring(6).trim();
+                        let matrixEnds = false;
+                        if (after.endsWith(';')) {
+                            matrixEnds = true;
+                            after = after.slice(0, -1).trim();
+                        }
+                        if (after.length > 0) {
+                            addMatrixRow(after);
+                        }
+                        if (matrixEnds) {
+                            inMatrix = false;
+                            inDataBlock = false;
+                            datatype = null;
+                        }
+                    }
+                } else {
+                    // inside the MATRIX: one taxon row per line until ';'
+                    let matrixEnds = false;
+                    if (line.endsWith(';')) {
+                        matrixEnds = true;
+                        line = line.slice(0, -1).trim();
+                    }
+                    if (line.length > 0) {
+                        addMatrixRow(line);
+                    }
+                    if (matrixEnds) {
+                        inMatrix = false;
+                        inDataBlock = false;
+                        datatype = null;
+                    }
                 }
             }
         }
+        finishTree(); // EOF with a tree still pending (no closing "End;")
+        return trees;
     };
 
-
-    /**
+    // ---------------------------------------------------------------
+    // Auspice / Nextstrain
+    // ---------------------------------------------------------------
+
+    // Namespace for the node properties the Auspice parser writes, so
+    // Nextstrain traits are colour-able/searchable and clearly distinguished
+    // from BEAST's "beast:" namespace. Same prefix as the desktop.
+    const NEXTSTRAIN_PREFIX = 'nextstrain:';
+
+    // A compact string for a JSON number: a whole value drops the ".0" (a
+    // clean categorical/integer property), otherwise the plain decimal
+    // WITHOUT scientific notation (a small divergence like 1e-4 must read
+    // as "0.0001" in the node-data dialog / as a searchable value).
+    function plainNumberString(d) {
+        if (Number.isInteger(d) && Math.abs(d) < 1e15) {
+            return String(d);
+        }
+        let s = String(d);
+        if (s.indexOf('e') < 0 && s.indexOf('E') < 0) {
+            return s;
+        }
+        return d.toFixed(20).replace(/0+$/, '').replace(/\.$/, '');
+    }
+
+    function addNodeProperty(node, ref, value) {
+        if (value === undefined || value === null || String(value).length === 0) {
+            return;
+        }
+        if (!node.properties) {
+            node.properties = [];
+        }
+        let v = String(value);
+        node.properties.push({
+            ref: ref,
+            value: v,
+            datatype: isFinite(parseFloat(v)) && isFinite(Number(v)) ? 'xsd:decimal' : 'xsd:string',
+            applies_to: 'node'
+        });
+    }
+
+    // Parses an Auspice / Nextstrain v2 dataset.json (string or already-parsed
+    // object) into ONE tree object, mapping its per-node data onto the native
+    // phyloXML shape so the existing overlays light it up -- ported from the
+    // desktop's AuspiceJsonParser:
+    //  - node_attrs.num_date.value -> node.date value (decimal year) -> the
+    //    calendar time axis; its .confidence [lo,hi] -> date minimum/maximum
+    //    -> the node-age (HPD) bars;
+    //  - node_attrs.div -> a nextstrain:div property (the divergence measure,
+    //    kept for a future time<->divergence view);
+    //  - every discrete trait (country, clade_membership, host, ...) -> a
+    //    nextstrain:<key> node property (Color-by / search / node dialog);
+    //    its .confidence {state:prob} -> nextstrain:<key>_set + _set_prob
+    //    brace-list pair (the desktop's ancestral-state-pie encoding);
+    //  - branch_attrs.labels.clade -> a nextstrain:clade_label property.
+    // Branch lengths default to TIME (successive num_date differences); a
+    // divergence-only build falls back to div differences. Deliberately NOT
+    // ingested: the map, entropy and frequencies panels.
+    forester.parseAuspiceJson = function (data) {
+        let doc = forester.isString(data) ? JSON.parse(data) : data;
+        if (!doc || typeof doc !== 'object' || Array.isArray(doc)) {
+            throw new Error('not an Auspice dataset (the JSON root is not an object)');
+        }
+        if (doc.version !== 'v2' || !doc.tree || typeof doc.tree !== 'object'
+            || Array.isArray(doc.tree)) {
+            throw new Error('not an Auspice v2 dataset (expected "version":"v2" and a "tree" object)');
+        }
+
+        function isScalar(v) {
+            return (typeof v === 'string') || (typeof v === 'number') || (typeof v === 'boolean');
+        }
+
+        function scalarToString(v) {
+            return (typeof v === 'number') ? plainNumberString(v) : String(v);
+        }
+
+        // a discrete trait's posterior distribution as the _set/_set_prob
+        // brace-list pair; state names quoted so a comma/space in one (e.g.
+        // "Korea, Republic of") cannot corrupt the list
+        function applyTraitConfidence(node, trait, conf) {
+            let states = [];
+            let probs = [];
+            Object.keys(conf).forEach(function (state) {
+                let p = conf[state];
+                if (typeof p !== 'number' || !isFinite(p) || state.length === 0) {
+                    return;
+                }
+                states.push('"' + state.replace(/"/g, '') + '"');
+                probs.push(plainNumberString(p));
+            });
+            if (states.length > 0) {
+                addNodeProperty(node, NEXTSTRAIN_PREFIX + trait + '_set', '{' + states.join(',') + '}');
+                addNodeProperty(node, NEXTSTRAIN_PREFIX + trait + '_set_prob', '{' + probs.join(',') + '}');
+            }
+        }
+
+        function applyNodeAttrs(node, attrs) {
+            Object.keys(attrs).forEach(function (key) {
+                let val = attrs[key];
+                if (key === 'num_date') {
+                    if (val && typeof val === 'object' && typeof val.value === 'number') {
+                        let date = {value: val.value, unit: 'year'};
+                        if (Array.isArray(val.confidence) && val.confidence.length === 2
+                            && typeof val.confidence[0] === 'number'
+                            && typeof val.confidence[1] === 'number') {
+                            date.minimum = val.confidence[0];
+                            date.maximum = val.confidence[1];
+                        }
+                        node.date = date;
+                        // the point date doubles as a numeric property, so the
+                        // sampling date can drive Color-by (the classic
+                        // Nextstrain colour-by-date view) and search
+                        addNodeProperty(node, NEXTSTRAIN_PREFIX + 'num_date', plainNumberString(val.value));
+                    }
+                } else if (key === 'div') {
+                    if (typeof val === 'number' && isFinite(val)) {
+                        addNodeProperty(node, NEXTSTRAIN_PREFIX + 'div', plainNumberString(val));
+                    }
+                } else if (val && typeof val === 'object' && !Array.isArray(val)) {
+                    // a discrete trait: {value, confidence{state:prob}, entropy}
+                    if (isScalar(val.value)) {
+                        addNodeProperty(node, NEXTSTRAIN_PREFIX + key, scalarToString(val.value));
+                    }
+                    if (val.confidence && typeof val.confidence === 'object'
+                        && !Array.isArray(val.confidence)) {
+                        applyTraitConfidence(node, key, val.confidence);
+                    }
+                } else if (isScalar(val)) {
+                    addNodeProperty(node, NEXTSTRAIN_PREFIX + key, scalarToString(val)); // bare attr (accession, url, ...)
+                }
+            });
+        }
+
+        function buildNode(jn) {
+            let node = {};
+            if (typeof jn.name === 'string' && jn.name.length > 0) {
+                node.name = jn.name;
+            }
+            if (jn.node_attrs && typeof jn.node_attrs === 'object') {
+                applyNodeAttrs(node, jn.node_attrs);
+            }
+            let labels = jn.branch_attrs && jn.branch_attrs.labels;
+            if (labels && typeof labels.clade === 'string' && labels.clade.length > 0) {
+                addNodeProperty(node, NEXTSTRAIN_PREFIX + 'clade_label', labels.clade);
+            }
+            if (Array.isArray(jn.children) && jn.children.length > 0) {
+                node.children = [];
+                jn.children.forEach(function (c) {
+                    if (c && typeof c === 'object') {
+                        node.children.push(buildNode(c));
+                    }
+                });
+                if (node.children.length === 0) {
+                    delete node.children;
+                }
+            }
+            return node;
+        }
+
+        let root = buildNode(doc.tree);
+        let phy = {rooted: true, children: [root]};
+        let title = doc.meta && doc.meta.title;
+        if (typeof title === 'string' && title.trim().length > 0) {
+            phy.name = title.trim();
+        }
+        if (auspiceHasAnyDate(root)) {
+            setDeltaBranchLengths(root, null, auspiceNodeDate); // default view = time
+        } else {
+            // a divergence-only build carries no num_date anywhere; div deltas
+            // keep the layout meaningful instead of a cladogram
+            setDeltaBranchLengths(root, null, auspiceNodeDiv);
+        }
+        // A TIP is a dated sample: keep its point date (the calendar axis)
+        // but drop the date INTERVAL -- the divergence-time uncertainty (the
+        // node-age bars) belongs to the INTERNAL nodes, and a tip interval
+        // would read as a fossil-style observed range on a viral tree.
+        forester.preOrderTraversalAll(root, function (n) {
+            if (!n.children && n.date
+                && (n.date.minimum !== undefined || n.date.maximum !== undefined)) {
+                n.date = {value: n.date.value, unit: n.date.unit};
+            }
+        });
+        forester.addParents(phy);
+        return phy;
+    };
+
+    function auspiceNodeDate(node) {
+        return (node.date && typeof node.date.value === 'number' && isFinite(node.date.value))
+            ? node.date.value : null;
+    }
+
+    function auspiceNodeDiv(node) {
+        if (node.properties) {
+            for (let i = 0; i < node.properties.length; ++i) {
+                if (node.properties[i].ref === NEXTSTRAIN_PREFIX + 'div') {
+                    let d = parseFloat(node.properties[i].value);
+                    return isFinite(d) ? d : null;
+                }
+            }
+        }
+        return null;
+    }
+
+    function auspiceHasAnyDate(node) {
+        let found = false;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (auspiceNodeDate(n) !== null) {
+                found = true;
+            }
+        });
+        return found;
+    }
+
+    function auspiceHasAnyDiv(node) {
+        let found = false;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (auspiceNodeDiv(n) !== null) {
+                found = true;
+            }
+        });
+        return found;
+    }
+
+    // Branch lengths = successive differences of a cumulative per-node metric
+    // (num_date -> the time view; nextstrain:div -> the divergence view).
+    // The root's length is 0, and a node missing the metric (or whose parent
+    // misses it) gets 0 -- so a time<->divergence toggle can never leave a
+    // stale cross-scale length behind. A (spurious) negative delta clamps to 0.
+    function setDeltaBranchLengths(node, parentValue, metricOf) {
+        let v = metricOf(node);
+        node.branch_length = (parentValue !== null && v !== null)
+            ? Math.max(0, v - parentValue) : 0;
+        let children = node.children || node._children;
+        if (children) {
+            for (let i = 0; i < children.length; ++i) {
+                setDeltaBranchLengths(children[i], v, metricOf);
+            }
+        }
+    }
+
+    // The time<->divergence plumbing: both metrics are RETAINED on a parsed
+    // Auspice tree (the date values + the nextstrain:div properties), so a
+    // future display toggle can rewrite the branch lengths from EITHER at any
+    // time -- lossless and reversible, and reusing the exact recompute the
+    // parser itself used, so the toggle can never drift from the loaded view.
+
+    forester.applyTimeBranchLengths = function (phy) {
+        setDeltaBranchLengths(forester.getTreeRoot(phy), null, auspiceNodeDate);
+    };
+
+    forester.applyDivergenceBranchLengths = function (phy) {
+        setDeltaBranchLengths(forester.getTreeRoot(phy), null, auspiceNodeDiv);
+    };
+
+    // True when the tree carries BOTH a time signal (a dated node) AND a
+    // divergence signal (a nextstrain:div property), so the toggle is
+    // meaningful at all.
+    forester.hasTimeAndDivergence = function (phy) {
+        let root = forester.getTreeRoot(phy);
+        return auspiceHasAnyDate(root) && auspiceHasAnyDiv(root);
+    };
+
+    forester.isNumber = function (v) {
+        if (v === undefined || v === null) {
+            return false;
+        }
+        if (v != v) {
+            // This can only be true if the v is NaN
+            return false;
+        }
+        return true;
+    };
+
+    forester.getOneDistinctTaxonomy = function (node) {
+        let id = null;
+        let code = null;
+        let sn = null;
+        let cn = null;
+        let result = true;
+        let sawTax = false;
+        forester.preOrderTraversalAll(node, function (n) {
+            if (n.taxonomies && n.taxonomies.length === 1) {
+                let tax = n.taxonomies[0];
+                if (tax.code && tax.code.length > 0) {
+                    sawTax = true;
+                    if (code === null) {
+                        code = tax.code;
+                    } else if (code !== tax.code) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.scientific_name && tax.scientific_name.length > 0) {
+                    sawTax = true;
+                    if (sn === null) {
+                        sn = tax.scientific_name;
+                    } else if (sn !== tax.scientific_name) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.common_name && tax.common_name.length > 0) {
+                    sawTax = true;
+                    if (cn === null) {
+                        cn = tax.common_name;
+                    } else if (cn !== tax.common_name) {
+                        result = false;
+                        return;
+                    }
+                }
+                if (tax.id && tax.id.value && tax.id.value.length > 0) {
+                    sawTax = true;
+                    let myid;
+                    if (tax.id.provider && tax.id.provider.length > 0) {
+                        myid = tax.id.provider + ':' + tax.id.value;
+                    } else {
+                        myid = tax.id.value;
+                    }
+                    if (id === null) {
+                        id = myid;
+                    } else if (id !== myid) {
+                        result = false;
+
+                    }
+                }
+            } else if (!n.children && !n._children) {
+                // If an external node lacks taxonomy, return false.
+                result = false;
+            }
+        });
+        if (!sawTax) {
+            return null;
+        }
+        if (result === true) {
+
+            if (sn) {
+                return sn;
+            } else if (code) {
+                return code;
+            } else if (cn) {
+                return cn;
+            } else if (id) {
+                return id;
+            }
+        }
+        return null;
+    };
+
+
+    /**
      * To convert a phylogentic tree object to a New Hampshire (Newick) formatted string.
      *
      * @param phy - A phylogentic tree object.
@@ -1664,7 +2983,7 @@
                     nh += replaceUnsafeChars(node.name);
                 } else {
                     let myName = node.name.replace(/\s+/g, ' ');
-                    if (/[\s,():;'"\[\]]/.test(myName)) {
+                    if (/[\s,():;'"[\]]/.test(myName)) {
                         if ((myName.indexOf('"') > -1) && (myName.indexOf("'") > -1)) {
                             nh += '"' + myName.replace(/"/g, "'") + '"';
                         } else if (myName.indexOf('"') > -1) {
@@ -1697,8 +3016,126 @@
         }
 
         function replaceUnsafeChars(str) {
-            return str.replace(/[\s,():;'"\[\]]+/g, '_');
+            return str.replace(/[\s,():;'"[\]]+/g, '_');
+        }
+    };
+
+    // Writes a phylogeny as a Nexus-formatted string, ported from the
+    // desktop's PhylogenyWriter: a TAXA block (Dimensions, TaxLabels) and a
+    // TREES block (the tree under its name, [&R]/[&U] rootedness, the same
+    // safe-character Newick toNewHampshire writes). Beyond the desktop
+    // template, tips carrying ALIGNED molecular sequences also get a
+    // CHARACTERS block (Dimensions, Format with the datatype, Matrix) --
+    // carrying the tree and its alignment in one file is the point of Nexus,
+    // and parseNexus reads the alignment back onto the tips.
+    forester.toNexus = function (phy, decPointsMax, writeConfidences) {
+        // the same replacement toNewHampshire applies, so the TaxLabels and
+        // Matrix labels match the tree's tip tokens exactly
+        function safeLabel(s) {
+            return s.replace(/[\s,():;'"[\]]+/g, '_');
+        }
+
+        // label preference as on the desktop: name, then taxonomy
+        // (code/scientific/common), then sequence (name/symbol/gene)
+        function nexusLabel(node, i) {
+            let s = '';
+            if (node.name) {
+                s = node.name;
+            } else if (node.taxonomies && node.taxonomies.length > 0) {
+                let t = node.taxonomies[0];
+                s = t.code || t.scientific_name || t.common_name || '';
+            } else if (node.sequences && node.sequences.length > 0) {
+                let q = node.sequences[0];
+                s = q.name || q.symbol || q.gene_name || '';
+            }
+            if (!s) {
+                s = 'node' + (i + 1); // an empty TaxLabels token would not parse back
+            }
+            return safeLabel(s);
+        }
+
+        let ext = forester.getAllExternalNodes(phy).reverse();
+        // a nameless tip gets its taxa-block label in the TREE as well --
+        // TaxLabels, the Matrix and the Newick must agree on every taxon or
+        // nothing can join them back up (restored before returning, so the
+        // caller's tree is never mutated)
+        let renamed = [];
+        ext.forEach(function (node, i) {
+            if (!node.name) {
+                node.name = nexusLabel(node, i);
+                renamed.push(node);
+            }
+        });
+        let s = '#NEXUS\n';
+        s += 'Begin Taxa;\n';
+        s += ' Dimensions NTax=' + ext.length + ';\n';
+        s += ' TaxLabels';
+        ext.forEach(function (node, i) {
+            s += ' ' + nexusLabel(node, i);
+        });
+        s += ';\n';
+        s += 'End;\n';
+
+        let rows = [];
+        let nchar = 0;
+        let datatype = null;
+        ext.forEach(function (node, i) {
+            if (!node.sequences) {
+                return;
+            }
+            for (let j = 0; j < node.sequences.length; ++j) {
+                let q = node.sequences[j];
+                if (q.mol_seq && q.mol_seq.is_aligned && q.mol_seq.value) {
+                    rows.push({label: nexusLabel(node, i), value: q.mol_seq.value});
+                    nchar = Math.max(nchar, q.mol_seq.value.length);
+                    if (!datatype && (q.type === 'protein' || q.type === 'dna' || q.type === 'rna')) {
+                        datatype = q.type;
+                    }
+                    return;
+                }
+            }
+        });
+        if (rows.length > 0) {
+            if (!datatype) {
+                // no declared type (e.g. the tree came from Newick plus a
+                // fasta): judge on the residues themselves
+                datatype = forester.msaIsNucleotide(rows[0].value) ? 'dna' : 'protein';
+            }
+            let width = 0;
+            rows.forEach(function (r) {
+                width = Math.max(width, r.label.length);
+            });
+            s += 'Begin Characters;\n';
+            // NChar ONLY: the Nexus standard allows NTax in a CHARACTERS
+            // block's DIMENSIONS solely alongside NEWTAXA (the taxa are the
+            // TAXA block's), and strict readers -- jebl, and so AliView --
+            // reject the file over it
+            s += ' Dimensions NChar=' + nchar + ';\n';
+            s += ' Format DataType=' + datatype + ' Missing=? Gap=-;\n';
+            s += ' Matrix\n';
+            rows.forEach(function (r) {
+                s += '  ' + r.label + ' '.repeat(width - r.label.length + 1) + r.value + '\n';
+            });
+            s += ' ;\n';
+            s += 'End;\n';
         }
+
+        s += 'Begin Trees;\n';
+        let treeName = phy.name ? String(phy.name).replace(/['"]+/g, '').trim() : '';
+        s += ' Tree ' + (treeName ? ("'" + treeName + "'") : 'tree1') + '=';
+        s += (phy.rooted === false) ? '[&U]' : '[&R]';
+        let nh = forester.toNewHampshire(phy, decPointsMax, true, writeConfidences);
+        renamed.forEach(function (node) {
+            delete node.name;
+        });
+        if (nh.length === 0) {
+            // an empty tree would otherwise write "Tree tree1=[&R]" with no
+            // tree and no terminating ';' -- a syntactically invalid file
+            throw new Error('toNexus: the tree is empty (nothing to write)');
+        }
+        s += nh + '\n';
+        s += 'End;\n';
+        return s;
     };
 
     forester.getMolecularSequencesAsFasta = function (node, sep) {
@@ -1741,6 +3178,1317 @@
     };
 
 
+    // --------------------------------------------------------------
+    // Search engine
+    // --------------------------------------------------------------
+    // Field-and-mode search over a phylogeny (mirrors the desktop Archaeopteryx
+    // redesign). A search is described by a spec:
+    //   { field, mode, value, value2, caseSensitive, inverse }
+    // where field comes from forester.availableSearchFields(root), mode is one of
+    // the string modes ('contains', 'starts_with', 'ends_with', 'whole_word',
+    // 'regex') or numeric modes ('eq', 'ne', 'lt', 'le', 'gt', 'ge', 'range'),
+    // and ',' = OR / '+' = AND inside a text value. Used by archaeopteryx.js;
+    // pure tree logic, no DOM -- tested by test/search_test.js.
+
+    const SEARCH_FIELD_LABELS = {
+        NN: 'Node Name',
+        TS: 'Taxonomy Scientific', TN: 'Taxonomy Common', TC: 'Taxonomy Code',
+        TI: 'Taxonomy Identifier', SY: 'Taxonomy Synonym', LN: 'Taxonomy Lineage',
+        SN: 'Seq Name', GN: 'Gene Name', SS: 'Gene Symbol', SA: 'Seq Accession',
+        MS: 'Molecular Sequence', DO: 'Domain', AN: 'Annotation', XR: 'Cross-Reference'
+    };
+    const SEARCH_TEXT_ORDER = ['TS', 'TN', 'TC', 'TI', 'SY', 'LN', 'SN', 'GN', 'SS', 'SA', 'DO', 'AN', 'XR', 'MS'];
+    // Fields folded into the "Any Text" umbrella (desktop omits MS + DO there).
+    const SEARCH_ANY_TEXT_KEYS = ['NN', 'TS', 'TN', 'TC', 'TI', 'SY', 'LN', 'SN', 'GN', 'SS', 'SA', 'AN', 'XR'];
+    const SEARCH_NUMERIC_DATATYPES = new Set(['decimal', 'double', 'float', 'integer', 'int', 'long', 'short',
+        'byte', 'unsignedint', 'unsignedlong', 'unsignedshort', 'unsignedbyte', 'nonnegativeinteger',
+        'nonpositiveinteger', 'negativeinteger', 'positiveinteger']);
+
+    function searchTaxa(n) { return (n.taxonomies && n.taxonomies.length) ? n.taxonomies : []; }
+    function searchSeqs(n) { return (n.sequences && n.sequences.length) ? n.sequences : []; }
+
+    const SEARCH_TEXT_EXTRACTORS = {
+        NN: n => (n.name ? [n.name] : []),
+        TS: n => searchTaxa(n).map(t => t.scientific_name).filter(Boolean),
+        TN: n => searchTaxa(n).map(t => t.common_name).filter(Boolean),
+        TC: n => searchTaxa(n).map(t => t.code).filter(Boolean),
+        TI: n => searchTaxa(n).map(t => t.id && t.id.value).filter(Boolean),
+        SY: n => searchTaxa(n).reduce((a, t) => a.concat(t.synonyms || []), []).filter(Boolean),
+        LN: n => searchTaxa(n).reduce((a, t) => a.concat(t.lineage || []), []).filter(Boolean),
+        SN: n => searchSeqs(n).map(s => s.name).filter(Boolean),
+        GN: n => searchSeqs(n).map(s => s.gene_name).filter(Boolean),
+        SS: n => searchSeqs(n).map(s => s.symbol).filter(Boolean),
+        SA: n => searchSeqs(n).map(s => s.accession && s.accession.value).filter(Boolean),
+        MS: n => searchSeqs(n).map(s => s.mol_seq).filter(Boolean),
+        DO: n => searchSeqs(n).reduce((a, s) => a.concat((s.domain_architecture && s.domain_architecture.domains) ? s.domain_architecture.domains.map(d => d.name) : []), []).filter(Boolean),
+        AN: n => searchSeqs(n).reduce((a, s) => a.concat((s.annotations || []).reduce((b, an) => b.concat([an.desc, an.ref]), [])), []).filter(Boolean),
+        XR: n => searchSeqs(n).reduce((a, s) => a.concat((s.cross_references || []).reduce((b, x) => b.concat([x.value, x.source, x.comment]), [])), []).filter(Boolean)
+    };
+
+    function isInternalPropRef(ref) { return !ref || ref.indexOf('aptx:') === 0; }
+
+    function datatypeIsNumeric(dt) {
+        if (!dt) return false;
+        let local = String(dt).toLowerCase();
+        let c = local.lastIndexOf(':');
+        if (c >= 0) local = local.substring(c + 1);
+        return SEARCH_NUMERIC_DATATYPES.has(local);
+    }
+
+    function escapeSearchRegExp(str) {
+        return String(str).replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+    }
+
+    // Accept comma as decimal separator when unambiguous (one comma, no period,
+    // and not the US thousands pattern comma+exactly-3-digits). Returns null if
+    // not a finite number.
+    forester.parseFiniteDouble = function (s) {
+        if (s === null || s === undefined) return null;
+        s = String(s).trim();
+        if (s.length === 0) return null;
+        if (s.indexOf('.') < 0 && (s.split(',').length - 1) === 1 && !/,\d{3}$/.test(s)) {
+            s = s.replace(',', '.');
+        }
+        let n = Number(s);
+        return isFinite(n) ? n : null;
+    };
+
+    // Build a predicate value -> bool for one text term. Returns null for an
+    // invalid regex (caller treats that as "never matches").
+    forester.makeSearchStringTest = function (term, mode, caseSensitive) {
+        if (mode === 'regex' || mode === 'whole_word') {
+            let src = (mode === 'whole_word')
+                ? ('(?<![\\p{L}\\p{N}])' + escapeSearchRegExp(term) + '(?![\\p{L}\\p{N}])')
+                : term;
+            let re;
+            try { re = new RegExp(src, caseSensitive ? 'u' : 'iu'); }
+            catch { return null; }
+            return s => (s !== null && s !== undefined && re.test(String(s)));
+        }
+        let t = caseSensitive ? term : term.toLowerCase();
+        return function (s) {
+            if (s === null || s === undefined) return false;
+            let str = caseSensitive ? String(s) : String(s).toLowerCase();
+            if (mode === 'starts_with') return str.indexOf(t) === 0;
+            if (mode === 'ends_with') return str.length >= t.length && str.lastIndexOf(t) === str.length - t.length;
+            return str.indexOf(t) >= 0; // contains
+        };
+    };
+
+    function numMatches(x, mode, a, lo, hi) {
+        switch (mode) {
+            case 'eq': return Math.abs(x - a) <= 1e-9 * Math.max(1, Math.abs(a));
+            case 'ne': return Math.abs(x - a) > 1e-9 * Math.max(1, Math.abs(a));
+            case 'lt': return x < a;
+            case 'le': return x <= a;
+            case 'gt': return x > a;
+            case 'ge': return x >= a;
+            case 'range': return x >= lo && x <= hi;
+            default: return false;
+        }
+    }
+
+    // The list of fields the given tree actually offers (drives the Field
+    // dropdowns). Always exposes Any Text + Node Name; adds the text, numeric
+    // and custom-property fields that are present, then structure fields.
+    forester.availableSearchFields = function (root) {
+        let fields = [];
+        fields.push({ key: 'ANY', label: 'Any Text', numeric: false });
+        fields.push({ key: 'NN', label: SEARCH_FIELD_LABELS.NN, numeric: false });
+        if (!root) return fields;
+
+        let present = {};
+        let hasBL = false, hasConf = false;
+        let propRefs = {}; // ref -> { num, tot, dtNum, dtStr }
+        forester.preOrderTraversalAll(root, function (n) {
+            for (let k = 0; k < SEARCH_TEXT_ORDER.length; ++k) {
+                let key = SEARCH_TEXT_ORDER[k];
+                if (!present[key] && SEARCH_TEXT_EXTRACTORS[key](n).length > 0) present[key] = true;
+            }
+            if (!hasBL && typeof n.branch_length === 'number' && n.branch_length >= 0) hasBL = true;
+            if (!hasConf && n.confidences) {
+                for (let i = 0; i < n.confidences.length; ++i) {
+                    if (typeof n.confidences[i].value === 'number') { hasConf = true; break; }
+                }
+            }
+            if (n.properties) {
+                for (let i = 0; i < n.properties.length; ++i) {
+                    let p = n.properties[i];
+                    if (isInternalPropRef(p.ref)) continue;
+                    let r = propRefs[p.ref] || (propRefs[p.ref] = { num: 0, tot: 0, dtNum: false, dtStr: false });
+                    r.tot++;
+                    if (forester.parseFiniteDouble(p.value) !== null) r.num++;
+                    if (p.datatype) { if (datatypeIsNumeric(p.datatype)) r.dtNum = true; else r.dtStr = true; }
+                }
+            }
+        });
+
+        for (let k = 0; k < SEARCH_TEXT_ORDER.length; ++k) {
+            let key = SEARCH_TEXT_ORDER[k];
+            if (present[key]) fields.push({ key: key, label: SEARCH_FIELD_LABELS[key], numeric: false });
+        }
+        if (hasBL) fields.push({ key: 'BL', label: 'Branch Length', numeric: true });
+        if (hasConf) fields.push({ key: 'CO', label: 'Confidence', numeric: true });
+        let refs = Object.keys(propRefs).sort();
+        for (let i = 0; i < refs.length; ++i) {
+            let r = propRefs[refs[i]];
+            let numeric = r.dtStr ? false : (r.dtNum ? true : (r.tot > 0 && r.num === r.tot));
+            fields.push({ key: 'PROP:' + refs[i], label: refs[i], numeric: numeric, propRef: refs[i] });
+        }
+        fields.push({ key: 'CS', label: 'Clade Size (tips)', numeric: true });
+        fields.push({ key: 'NC', label: 'Number of Children', numeric: true });
+        fields.push({ key: 'DE', label: 'Depth from Root', numeric: true });
+        if (hasBL) fields.push({ key: 'DR', label: 'Distance from Root', numeric: true });
+        fields.push({ key: 'NT', label: 'Node Type', numeric: false });
+        return fields;
+    };
+
+    // Per-node depth / distance-to-root / clade size, computed on demand for the
+    // structure search fields (cheap O(n), avoids staleness after tree edits).
+    function computeSearchMetrics(root) {
+        (function pre(n, depth, dist) {
+            n._srchDepth = depth;
+            let d = dist + (typeof n.branch_length === 'number' && n.branch_length > 0 ? n.branch_length : 0);
+            n._srchDist = d;
+            let kids = n.children || n._children;
+            if (kids) for (let i = 0; i < kids.length; ++i) pre(kids[i], depth + 1, d);
+        })(root, 0, 0);
+        forester.postOrderTraversalAll(root, function (n) {
+            let kids = n.children || n._children;
+            if (!kids || kids.length === 0) { n._srchClade = 1; return; }
+            let s = 0;
+            for (let i = 0; i < kids.length; ++i) s += kids[i]._srchClade;
+            n._srchClade = s;
+        });
+    }
+
+    // Extract the value(s) of a field from a node (strings for text fields,
+    // numbers for the numeric ones). A field is multi-valued; any value matching
+    // is a match. root is needed only for the Node Type field.
+    forester.extractSearchValues = function (node, field, root) {
+        let key = field.key;
+        if (key === 'ANY') {
+            let out = [];
+            for (let i = 0; i < SEARCH_ANY_TEXT_KEYS.length; ++i) {
+                out = out.concat(SEARCH_TEXT_EXTRACTORS[SEARCH_ANY_TEXT_KEYS[i]](node));
+            }
+            if (node.properties) {
+                for (let i = 0; i < node.properties.length; ++i) {
+                    let p = node.properties[i];
+                    if (!isInternalPropRef(p.ref) && p.value !== null && p.value !== undefined && p.value !== '') out.push(p.value);
+                }
+            }
+            return out;
+        }
+        if (key === 'NT') {
+            let kids = node.children || node._children;
+            let isLeaf = !kids || kids.length === 0;
+            return [isLeaf ? 'leaf' : (node === root ? 'root' : 'internal')];
+        }
+        if (key.indexOf('PROP:') === 0) {
+            let out = [];
+            if (node.properties) {
+                for (let i = 0; i < node.properties.length; ++i) {
+                    let p = node.properties[i];
+                    if (p.ref === field.propRef && p.value !== null && p.value !== undefined && p.value !== '') out.push(p.value);
+                }
+            }
+            return out;
+        }
+        if (SEARCH_TEXT_EXTRACTORS[key]) return SEARCH_TEXT_EXTRACTORS[key](node);
+        switch (key) {
+            case 'BL': return (typeof node.branch_length === 'number') ? [node.branch_length] : [];
+            case 'CO': return node.confidences ? node.confidences.map(c => c.value).filter(v => typeof v === 'number') : [];
+            case 'CS': return [node._srchClade];
+            case 'NC': { let kids = node.children || node._children; return [kids ? kids.length : 0]; }
+            case 'DE': return [node._srchDepth];
+            case 'DR': return [node._srchDist];
+            default: return [];
+        }
+    };
+
+    // Run one search spec { field, mode, value, value2, caseSensitive, inverse }
+    // over the tree and return the Set of matching nodes.
+    // A parsed tree is anchored on a SUPER-ROOT: a synthetic node whose single
+    // child is the tree's actual root. It is not a node of the phylogeny -- it
+    // exists to give the root a parent slot, which is what lets reRoot() move
+    // the root around and what toNewHampshire() writes from. Both formats have
+    // one; from phyloXML it also carries the <phylogeny> element's own name and
+    // description, so it looks like a node with the TREE's name on it.
+    //
+    // Anything that reasons about the phylogeny's own nodes has to step over it.
+    // This is the test getTreeRoot uses, minus that function's walk UP the tree,
+    // which would escape a subtree a caller had deliberately scoped to.
+    function realRootOf(root) {
+        if (!root.parent && root.children && root.children.length === 1) {
+            return root.children[0];
+        }
+        return root;
+    }
+
+    forester.searchWithSpec = function (root, spec) {
+        let result = new Set();
+        if (!root || !spec || !spec.field) return result;
+        // Metrics stay relative to what the caller passed, so depth and distance
+        // values are unchanged; only the set of nodes considered is narrowed.
+        let nodes = realRootOf(root);
+        let field = spec.field;
+        if (field.key === 'CS' || field.key === 'DE' || field.key === 'DR' || field.key === 'NC') computeSearchMetrics(root);
+
+        let v = (spec.value === null || spec.value === undefined) ? '' : String(spec.value);
+        v = v.replace(/\s+/g, ' ').trim();
+
+        let test = null;
+        if (field.numeric) {
+            let a = forester.parseFiniteDouble(v);
+            let b = (spec.mode === 'range') ? forester.parseFiniteDouble(spec.value2) : null;
+            if (a === null || (spec.mode === 'range' && b === null)) return result; // invalid -> reset
+            let lo = (b !== null) ? Math.min(a, b) : a;
+            let hi = (b !== null) ? Math.max(a, b) : a;
+            test = function (n) {
+                let vals = forester.extractSearchValues(n, field, root);
+                for (let i = 0; i < vals.length; ++i) {
+                    let x = (typeof vals[i] === 'number') ? vals[i] : forester.parseFiniteDouble(vals[i]);
+                    if (x !== null && numMatches(x, spec.mode, a, lo, hi)) return true;
+                }
+                return false;
+            };
+        } else {
+            if (v.length < 1) return result;
+            let splittable = spec.mode !== 'regex';
+            let orTerms = (splittable && v.indexOf(',') >= 0) ? v.split(/,+/) : [v];
+            let compiled = [];
+            for (let oi = 0; oi < orTerms.length; ++oi) {
+                let ot = orTerms[oi].trim();
+                if (!ot) continue;
+                let ands = (splittable && ot.indexOf('+') > 0) ? ot.split(/\++/) : [ot];
+                let tests = [];
+                let bad = false;
+                for (let ai = 0; ai < ands.length; ++ai) {
+                    let term = ands[ai].trim();
+                    if (!term) continue;
+                    let t = forester.makeSearchStringTest(term, spec.mode, spec.caseSensitive);
+                    if (t === null) { bad = true; break; } // invalid regex
+                    tests.push(t);
+                }
+                if (!bad && tests.length) compiled.push(tests);
+            }
+            if (!compiled.length) return result;
+            test = function (n) {
+                let vals = forester.extractSearchValues(n, field, root);
+                for (let oi = 0; oi < compiled.length; ++oi) {
+                    let ands = compiled[oi], ok = true;
+                    for (let ai = 0; ai < ands.length; ++ai) {
+                        let hit = false;
+                        for (let vi = 0; vi < vals.length; ++vi) { if (ands[ai](vals[vi])) { hit = true; break; } }
+                        if (!hit) { ok = false; break; }
+                    }
+                    if (ok) return true;
+                }
+                return false;
+            };
+        }
+
+        forester.preOrderTraversalAll(nodes, function (n) { if (test(n)) result.add(n); });
+
+        if (spec.inverse) {
+            // Complement, scoped to nodes that actually carry this field.
+            let inv = new Set();
+            forester.preOrderTraversalAll(nodes, function (n) {
+                if (!result.has(n) && forester.extractSearchValues(n, field, root).length > 0) inv.add(n);
+            });
+            return inv;
+        }
+        return result;
+    };
+
+    // Distinct, trimmed, sorted values of a specific text field across the tree,
+    // for the value-box autocomplete. Empty for numeric, Any Text, or Molecular
+    // Sequence (near-unique / huge). cap limits the list length (optional).
+    forester.distinctSearchValues = function (root, field, cap) {
+        if (!root || !field || field.numeric || field.key === 'ANY' || field.key === 'MS') return [];
+        let set = new Set();
+        forester.preOrderTraversalAll(root, function (n) {
+            let vals = forester.extractSearchValues(n, field, root);
+            for (let i = 0; i < vals.length; ++i) {
+                if (vals[i] !== null && vals[i] !== undefined) {
+                    let v = String(vals[i]).trim();
+                    if (v.length > 0) set.add(v);
+                }
+            }
+        });
+        let arr = Array.from(set).sort(function (a, b) { return a.localeCompare(b); });
+        if (cap && arr.length > cap) arr = arr.slice(0, cap);
+        return arr;
+    };
+
+
+    // --------------------------------------------------------------
+    // Geologic time scale + time-tree detection (the desktop's time axes)
+    // --------------------------------------------------------------
+    // The ICS International Chronostratigraphic Chart as the desktop embeds
+    // it (GeologicTimeScale.java): {name, young, old, color}, ages in Ma,
+    // colours the official ICS ones (kept even in monochrome exports -- the
+    // timescale IS a colour key). Reference: Cohen, K.M., Harper, D.A.T.,
+    // Gibbard, P.L. & Car, N. (2025, updated), The ICS International
+    // Chronostratigraphic Chart this decade, Episodes 48: 105-115;
+    // International Commission on Stratigraphy, www.stratigraphy.org.
+
+    const GEO_SCALE = {
+        eon: [
+            {name: 'Phanerozoic', young: 0, old: 538.8, color: '#9AD9DD'},
+            {name: 'Proterozoic', young: 538.8, old: 2500, color: '#FF70B8'},
+            {name: 'Archean', young: 2500, old: 4031, color: '#FF3399'}
+        ],
+        era: [
+            {name: 'Cenozoic', young: 0, old: 66, color: '#F2F91D'},
+            {name: 'Mesozoic', young: 66, old: 251.902, color: '#67C5CA'},
+            {name: 'Paleozoic', young: 251.902, old: 538.8, color: '#99C08D'},
+            {name: 'Neoproterozoic', young: 538.8, old: 1000, color: '#FF9BCD'},
+            {name: 'Mesoproterozoic', young: 1000, old: 1600, color: '#FF7EBF'},
+            {name: 'Paleoproterozoic', young: 1600, old: 2500, color: '#E665A6'},
+            {name: 'Neoarchean', young: 2500, old: 2800, color: '#FF5CAD'},
+            {name: 'Mesoarchean', young: 2800, old: 3200, color: '#E62E8A'},
+            {name: 'Paleoarchean', young: 3200, old: 3600, color: '#CC297A'},
+            {name: 'Eoarchean', young: 3600, old: 4031, color: '#B2246B'}
+        ],
+        period: [
+            {name: 'Quaternary', young: 0, old: 2.58, color: '#F9F97F'},
+            {name: 'Neogene', young: 2.58, old: 23.04, color: '#FFE619'},
+            {name: 'Paleogene', young: 23.04, old: 66, color: '#FD9A52'},
+            {name: 'Cretaceous', young: 66, old: 143.1, color: '#7FC64E'},
+            {name: 'Jurassic', young: 143.1, old: 201.4, color: '#34B2C9'},
+            {name: 'Triassic', young: 201.4, old: 251.902, color: '#812B92'},
+            {name: 'Permian', young: 251.902, old: 298.9, color: '#F04028'},
+            {name: 'Carboniferous', young: 298.9, old: 358.86, color: '#67A599'},
+            {name: 'Devonian', young: 358.86, old: 419.62, color: '#CB8C37'},
+            {name: 'Silurian', young: 419.62, old: 443.1, color: '#B3E1B6'},
+            {name: 'Ordovician', young: 443.1, old: 486.85, color: '#009270'},
+            {name: 'Cambrian', young: 486.85, old: 538.8, color: '#7FA056'},
+            {name: 'Ediacaran', young: 538.8, old: 635, color: '#FFC3E1'},
+            {name: 'Cryogenian', young: 635, old: 720, color: '#FFAFD7'},
+            {name: 'Tonian', young: 720, old: 1000, color: '#FFA5D2'},
+            {name: 'Stenian', young: 1000, old: 1200, color: '#FFA5D2'},
+            {name: 'Ectasian', young: 1200, old: 1400, color: '#FF98CC'},
+            {name: 'Calymmian', young: 1400, old: 1600, color: '#FF8BC5'},
+            {name: 'Statherian', young: 1600, old: 1800, color: '#EE93C1'},
+            {name: 'Orosirian', young: 1800, old: 2050, color: '#E874AF'},
+            {name: 'Rhyacian', young: 2050, old: 2300, color: '#EB84B8'},
+            {name: 'Siderian', young: 2300, old: 2500, color: '#E874AF'}
+        ],
+        epoch: [
+            {name: 'Holocene', young: 0, old: 0.0117, color: '#FEF2E0'},
+            {name: 'Pleistocene', young: 0.0117, old: 2.58, color: '#FFF2AE'},
+            {name: 'Pliocene', young: 2.58, old: 5.333, color: '#FFFF99'},
+            {name: 'Miocene', young: 5.333, old: 23.04, color: '#FFFF00'},
+            {name: 'Oligocene', young: 23.04, old: 33.9, color: '#FDC07A'},
+            {name: 'Eocene', young: 33.9, old: 56, color: '#FDB46C'},
+            {name: 'Paleocene', young: 56, old: 66, color: '#FDA75F'},
+            {name: 'Late Cretaceous', young: 66, old: 100.5, color: '#A6D84A'},
+            {name: 'Early Cretaceous', young: 100.5, old: 143.1, color: '#8CCD57'},
+            {name: 'Late Jurassic', young: 143.1, old: 161.5, color: '#B3E3EE'},
+            {name: 'Middle Jurassic', young: 161.5, old: 174.7, color: '#80CFD8'},
+            {name: 'Early Jurassic', young: 174.7, old: 201.4, color: '#42AED0'},
+            {name: 'Late Triassic', young: 201.4, old: 237, color: '#BD8CC3'},
+            {name: 'Middle Triassic', young: 237, old: 246.7, color: '#B168B1'},
+            {name: 'Early Triassic', young: 246.7, old: 251.902, color: '#983999'},
+            {name: 'Lopingian', young: 251.902, old: 259.51, color: '#FBA794'},
+            {name: 'Guadalupian', young: 259.51, old: 274.4, color: '#FB745C'},
+            {name: 'Cisuralian', young: 274.4, old: 298.9, color: '#EF5845'},
+            {name: 'Pennsylvanian', young: 298.9, old: 323.4, color: '#99C2B5'},
+            {name: 'Mississippian', young: 323.4, old: 358.86, color: '#678F66'},
+            {name: 'Late Devonian', young: 358.86, old: 382.31, color: '#F1E19D'},
+            {name: 'Middle Devonian', young: 382.31, old: 393.47, color: '#F1C868'},
+            {name: 'Early Devonian', young: 393.47, old: 419.62, color: '#E5AC4D'},
+            {name: 'Pridoli', young: 419.62, old: 422.7, color: '#E6F5E1'},
+            {name: 'Ludlow', young: 422.7, old: 426.7, color: '#BFE6CF'},
+            {name: 'Wenlock', young: 426.7, old: 432.9, color: '#B3E1C2'},
+            {name: 'Llandovery', young: 432.9, old: 443.1, color: '#99D7B3'},
+            {name: 'Late Ordovician', young: 443.1, old: 458.2, color: '#7FCA93'},
+            {name: 'Middle Ordovician', young: 458.2, old: 471.3, color: '#4DB47E'},
+            {name: 'Early Ordovician', young: 471.3, old: 486.85, color: '#1A9D6F'},
+            {name: 'Furongian', young: 486.85, old: 497, color: '#B3E095'},
+            {name: 'Miaolingian', young: 497, old: 506.5, color: '#A6CF86'},
+            {name: 'Series 2', young: 506.5, old: 521, color: '#99C078'},
+            {name: 'Terreneuvian', young: 521, old: 538.8, color: '#8CB06C'}
+        ],
+        // The 101 ratified Phanerozoic stages, plus the Pridoli: a Series with
+        // no stages of its own, standing in the stage row for its own span
+        // (419.62-422.7 Ma) as on the printed ICS chart -- without it the row
+        // would have a hole there. Same source as every rank above
+        // (Macrostrat international timescale, id 11), which the ranks above
+        // match byte for byte; the desktop generated its table from the same
+        // query, so the two programs band from identical data.
+        age: [
+            {name: 'Meghalayan', young: 0, old: 0.0042, color: '#FEF2E0'},
+            {name: 'Northgrippian', young: 0.0042, old: 0.0082, color: '#FEF2E0'},
+            {name: 'Greenlandian', young: 0.0082, old: 0.0117, color: '#FEF2E0'},
+            {name: 'Late Pleistocene', young: 0.0117, old: 0.129, color: '#FFF2C7'},
+            {name: 'Chibanian', young: 0.129, old: 0.774, color: '#FFF2C7'},
+            {name: 'Calabrian', young: 0.774, old: 1.8, color: '#FFF2C7'},
+            {name: 'Gelasian', young: 1.8, old: 2.58, color: '#FFEDB3'},
+            {name: 'Piacenzian', young: 2.58, old: 3.6, color: '#FFFFBF'},
+            {name: 'Zanclean', young: 3.6, old: 5.333, color: '#FFFFB3'},
+            {name: 'Messinian', young: 5.333, old: 7.246, color: '#FFFF73'},
+            {name: 'Tortonian', young: 7.246, old: 11.63, color: '#FFFF66'},
+            {name: 'Serravallian', young: 11.63, old: 13.82, color: '#FFFF59'},
+            {name: 'Langhian', young: 13.82, old: 15.98, color: '#FFFF4D'},
+            {name: 'Burdigalian', young: 15.98, old: 20.45, color: '#FFFF41'},
+            {name: 'Aquitanian', young: 20.45, old: 23.04, color: '#FFFF33'},
+            {name: 'Chattian', young: 23.04, old: 27.3, color: '#FEE6AA'},
+            {name: 'Rupelian', young: 27.3, old: 33.9, color: '#FED99A'},
+            {name: 'Priabonian', young: 33.9, old: 37.71, color: '#FDCDA1'},
+            {name: 'Bartonian', young: 37.71, old: 41.03, color: '#FDC091'},
+            {name: 'Lutetian', young: 41.03, old: 48.07, color: '#FCB482'},
+            {name: 'Ypresian', young: 48.07, old: 56, color: '#FCA773'},
+            {name: 'Thanetian', young: 56, old: 59.24, color: '#FDBF6F'},
+            {name: 'Selandian', young: 59.24, old: 61.66, color: '#FEBF65'},
+            {name: 'Danian', young: 61.66, old: 66, color: '#FDB462'},
+            {name: 'Maastrichtian', young: 66, old: 72.2, color: '#F2FA8C'},
+            {name: 'Campanian', young: 72.2, old: 83.6, color: '#E6F47F'},
+            {name: 'Santonian', young: 83.6, old: 85.7, color: '#D9EF74'},
+            {name: 'Coniacian', young: 85.7, old: 89.8, color: '#CCE968'},
+            {name: 'Turonian', young: 89.8, old: 93.9, color: '#BFE35D'},
+            {name: 'Cenomanian', young: 93.9, old: 100.5, color: '#B3DE53'},
+            {name: 'Albian', young: 100.5, old: 113.2, color: '#CCEA97'},
+            {name: 'Aptian', young: 113.2, old: 121.4, color: '#BFE48A'},
+            {name: 'Barremian', young: 121.4, old: 125.77, color: '#B3DF7F'},
+            {name: 'Hauterivian', young: 125.77, old: 132.6, color: '#A6D975'},
+            {name: 'Valanginian', young: 132.6, old: 137.05, color: '#99D36A'},
+            {name: 'Berriasian', young: 137.05, old: 143.1, color: '#8CCD60'},
+            {name: 'Tithonian', young: 143.1, old: 149.2, color: '#D9F1F7'},
+            {name: 'Kimmeridgian', young: 149.2, old: 154.8, color: '#CCECF4'},
+            {name: 'Oxfordian', young: 154.8, old: 161.5, color: '#BFE7F1'},
+            {name: 'Callovian', young: 161.5, old: 165.3, color: '#BFE7E5'},
+            {name: 'Bathonian', young: 165.3, old: 168.2, color: '#B3E2E3'},
+            {name: 'Bajocian', young: 168.2, old: 170.9, color: '#A6DDE0'},
+            {name: 'Aalenian', young: 170.9, old: 174.7, color: '#9AD9DD'},
+            {name: 'Toarcian', young: 174.7, old: 184.2, color: '#99CEE3'},
+            {name: 'Pliensbachian', young: 184.2, old: 192.9, color: '#80C5DD'},
+            {name: 'Sinemurian', young: 192.9, old: 199.5, color: '#67BCD8'},
+            {name: 'Hettangian', young: 199.5, old: 201.4, color: '#4EB3D3'},
+            {name: 'Rhaetian', young: 201.4, old: 205.7, color: '#E3B9DB'},
+            {name: 'Norian', young: 205.7, old: 227.3, color: '#D6AAD3'},
+            {name: 'Carnian', young: 227.3, old: 237, color: '#C99BCB'},
+            {name: 'Ladinian', young: 237, old: 241.464, color: '#C983BF'},
+            {name: 'Anisian', young: 241.464, old: 246.7, color: '#BC75B7'},
+            {name: 'Olenekian', young: 246.7, old: 249.9, color: '#B051A5'},
+            {name: 'Induan', young: 249.9, old: 251.902, color: '#A4469F'},
+            {name: 'Changhsingian', young: 251.902, old: 254.14, color: '#FCC0B2'},
+            {name: 'Wuchiapingian', young: 254.14, old: 259.51, color: '#FCB4A2'},
+            {name: 'Capitanian', young: 259.51, old: 264.28, color: '#FB9A85'},
+            {name: 'Wordian', young: 264.28, old: 266.9, color: '#FB8D76'},
+            {name: 'Roadian', young: 266.9, old: 274.4, color: '#FB8069'},
+            {name: 'Kungurian', young: 274.4, old: 283.3, color: '#E38776'},
+            {name: 'Artinskian', young: 283.3, old: 290.1, color: '#E37B68'},
+            {name: 'Sakmarian', young: 290.1, old: 293.52, color: '#E36F5C'},
+            {name: 'Asselian', young: 293.52, old: 298.9, color: '#E36350'},
+            {name: 'Gzhelian', young: 298.9, old: 303.7, color: '#CCD4C7'},
+            {name: 'Kasimovian', young: 303.7, old: 307, color: '#BFD0C5'},
+            {name: 'Moscovian', young: 307, old: 315.2, color: '#C7CBB9'},
+            {name: 'Bashkirian', young: 315.2, old: 323.4, color: '#99C2B5'},
+            {name: 'Serpukhovian', young: 323.4, old: 330.3, color: '#BFC26B'},
+            {name: 'Visean', young: 330.3, old: 346.7, color: '#A6B96C'},
+            {name: 'Tournaisian', young: 346.7, old: 358.86, color: '#8CB06C'},
+            {name: 'Famennian', young: 358.86, old: 372.15, color: '#F2EDC5'},
+            {name: 'Frasnian', young: 372.15, old: 382.31, color: '#F2EDAD'},
+            {name: 'Givetian', young: 382.31, old: 387.95, color: '#F1E185'},
+            {name: 'Eifelian', young: 387.95, old: 393.47, color: '#F1D576'},
+            {name: 'Emsian', young: 393.47, old: 410.62, color: '#E5D075'},
+            {name: 'Pragian', young: 410.62, old: 413.02, color: '#E5C468'},
+            {name: 'Lochkovian', young: 413.02, old: 419.62, color: '#E5B75A'},
+            {name: 'Pridoli', young: 419.62, old: 422.7, color: '#E6F5E1'},
+            {name: 'Ludfordian', young: 422.7, old: 425, color: '#D9F0DF'},
+            {name: 'Gorstian', young: 425, old: 426.7, color: '#CCECDD'},
+            {name: 'Homerian', young: 426.7, old: 430.6, color: '#CCEBD1'},
+            {name: 'Sheinwoodian', young: 430.6, old: 432.9, color: '#BFE6C3'},
+            {name: 'Telychian', young: 432.9, old: 438.6, color: '#BFE6CF'},
+            {name: 'Aeronian', young: 438.6, old: 440.5, color: '#B3E1C2'},
+            {name: 'Rhuddanian', young: 440.5, old: 443.1, color: '#A6DCB5'},
+            {name: 'Hirnantian', young: 443.1, old: 445.2, color: '#A6DBAB'},
+            {name: 'Katian', young: 445.2, old: 452.8, color: '#99D69F'},
+            {name: 'Sandbian', young: 452.8, old: 458.2, color: '#8CD094'},
+            {name: 'Darriwilian', young: 458.2, old: 469.4, color: '#74C69C'},
+            {name: 'Dapingian', young: 469.4, old: 471.3, color: '#66C092'},
+            {name: 'Floian', young: 471.3, old: 477.1, color: '#41B087'},
+            {name: 'Tremadocian', young: 477.1, old: 486.85, color: '#33A97E'},
+            {name: 'Stage 10', young: 486.85, old: 491, color: '#E6F5C9'},
+            {name: 'Jiangshanian', young: 491, old: 494.2, color: '#D9F0BB'},
+            {name: 'Paibian', young: 494.2, old: 497, color: '#CCEBAE'},
+            {name: 'Guzhangian', young: 497, old: 500.5, color: '#CCDFAA'},
+            {name: 'Drumian', young: 500.5, old: 504.5, color: '#BFD99D'},
+            {name: 'Wuliuan', young: 504.5, old: 506.5, color: '#B3D492'},
+            {name: 'Stage 4', young: 506.5, old: 514.5, color: '#B3CA8E'},
+            {name: 'Stage 3', young: 514.5, old: 521, color: '#A6C583'},
+            {name: 'Stage 2', young: 521, old: 529, color: '#A6BA80'},
+            {name: 'Fortunian', young: 529, old: 538.8, color: '#99B575'}
+        ]
+    };
+
+    forester.geoIntervals = function (rank) {
+        return GEO_SCALE[rank] || [];
+    };
+
+    // How far back a rank's intervals reach (its oldest boundary, Ma).
+    forester.geoCoverage = function (rank) {
+        let ivs = forester.geoIntervals(rank);
+        return ivs.length > 0 ? ivs[ivs.length - 1].old : 0;
+    };
+
+    // The [coarse, fine] rank pair for the span [youngMa, oldMa] a tree
+    // actually occupies -- the youngest tip to the root, not 0 to the root,
+    // so a fossil-only clade bands on its own window rather than on the
+    // whole stretch back from the present.
+    //
+    // It adapts FINER as well as coarser. A narrow Phanerozoic window --
+    // one or two Series -- bands Series over STAGE (the ICS ages), which is
+    // what a 66-100 Ma dinosaur tree needs to say anything at all: over
+    // Period/Epoch it would read "Cretaceous / Late Cretaceous" and nothing
+    // more. Wider than two Series the stages would be slivers, so the
+    // existing ladder takes over: the finest pair that still fully covers the
+    // range, so a deep tree never shows blank band segments. Shared rule with
+    // the desktop's GeologicTimeScale.bandRanks -- change both or neither.
+    forester.geoBandRanks = function (youngMa, oldMa) {
+        if (oldMa <= forester.geoCoverage('age')) {   // stages are Phanerozoic-only
+            let series = forester.geoOverlapping('epoch', youngMa, oldMa).length;
+            if (series > 0 && series <= 2) {
+                return ['epoch', 'age'];
+            }
+        }
+        if (oldMa <= forester.geoCoverage('epoch')) {
+            return ['period', 'epoch'];
+        }
+        if (oldMa <= forester.geoCoverage('period')) {
+            return ['era', 'period'];
+        }
+        return ['eon', 'era'];
+    };
+
+    // The rank's intervals overlapping [youngMa, oldMa] (a zero-width window
+    // becomes a point query).
+    forester.geoOverlapping = function (rank, youngMa, oldMa) {
+        let lo = Math.min(youngMa, oldMa);
+        let hi = Math.max(youngMa, oldMa);
+        return forester.geoIntervals(rank).filter(function (iv) {
+            if (hi === lo) {
+                return iv.young <= lo && lo < iv.old;
+            }
+            return iv.old > lo && iv.young < hi;
+        });
+    };
+
+    // The rank's interval containing ageMa (young <= age < old), or null.
+    forester.geoAt = function (rank, ageMa) {
+        let ivs = forester.geoIntervals(rank);
+        for (let i = 0; i < ivs.length; ++i) {
+            if (ivs[i].young <= ageMa && ageMa < ivs[i].old) {
+                return ivs[i];
+            }
+        }
+        return null;
+    };
+
+    // ---- time-tree detection -------------------------------------------
+    // Two date conventions: GEOLOGIC ages (Ma before present, decreasing
+    // toward the tips) and CALENDAR years (increasing toward the tips).
+    // Decided from the <date> unit attributes, with a magnitude fallback for
+    // unitless dates: values mostly in [1500, 2200] read as years; values
+    // spanning from large down toward ~0 read as ages.
+    const GEO_DATE_UNITS = {
+        mya: 1, ma: 1, myr: 1, myrs: 1, my: 1, ga: 1, gya: 1, bya: 1, kya: 1,
+        'million years': 1, 'billion years': 1
+    };
+    const CAL_DATE_UNITS = {
+        year: 1, years: 1, yr: 1, yrs: 1, cal: 1, ce: 1, ad: 1, calendar: 1,
+        'calendar year': 1, 'calendar years': 1
+    };
+
+    // Everything the viewer needs to decide about and draw a time axis:
+    // {type: 'geologic'|'calendar'|null, rootAge, presentDate, dated,
+    //  hasInternalIntervals, hasExternalIntervals}. rootAge (geologic) and
+    // presentDate (calendar) are both the LARGEST date value -- the oldest
+    // node for ages, the most recent tip for years.
+    forester.timeAxisInfo = function (root) {
+        let values = [];
+        let maxVal = -Infinity; // running, not Math.max.apply: 150k dated tips overflow the call stack
+        let minVal = Infinity;
+        let geoUnits = 0;
+        let calUnits = 0;
+        let internal = 0;
+        let external = 0;
+        let datedInternal = 0;
+        let datedExternal = 0;
+        let hasInternalIntervals = false;
+        let hasExternalIntervals = false;
+        forester.preOrderTraversalAll(root, function (n) {
+            let isExt = !n.children && !n._children;
+            if (isExt) {
+                ++external;
+            } else {
+                ++internal;
+            }
+            let d = n.date;
+            if (!d) {
+                return;
+            }
+            let interval = (typeof d.minimum === 'number') && (typeof d.maximum === 'number');
+            if (interval) {
+                if (isExt) {
+                    hasExternalIntervals = true;
+                } else {
+                    hasInternalIntervals = true;
+                }
+            }
+            if (typeof d.value !== 'number' || !isFinite(d.value)) {
+                return; // 1e400 parses to Infinity and must never reach the tick loops
+            }
+            values.push(d.value);
+            if (d.value > maxVal) {
+                maxVal = d.value;
+            }
+            if (d.value < minVal) {
+                minVal = d.value;
+            }
+            if (isExt) {
+                ++datedExternal;
+            } else {
+                ++datedInternal;
+            }
+            if (d.unit) {
+                let u = String(d.unit).trim().toLowerCase();
+                if (GEO_DATE_UNITS[u]) {
+                    ++geoUnits;
+                } else if (CAL_DATE_UNITS[u]) {
+                    ++calUnits;
+                }
+            }
+        });
+        let type = null;
+        if (values.length > 0) {
+            if (geoUnits > 0 && geoUnits >= calUnits) {
+                type = 'geologic';
+            } else if (calUnits > 0) {
+                type = 'calendar';
+            } else {
+                let calendarish = values.filter(function (v) {
+                    return v >= 1500 && v <= 2200;
+                }).length;
+                if (calendarish * 2 > values.length) {
+                    type = 'calendar';
+                } else if (maxVal > 10 && minVal <= maxVal * 0.05) {
+                    type = 'geologic';
+                }
+            }
+        }
+        let dated = (datedInternal >= 2 && (datedInternal * 2) > internal)
+            || (datedExternal >= 2 && (datedExternal * 2) > external);
+        let maxValue = values.length > 0 ? maxVal : 0;
+        return {
+            type: type,
+            rootAge: type === 'geologic' ? maxValue : 0,
+            presentDate: type === 'calendar' ? maxValue : 0,
+            dated: dated,
+            hasInternalIntervals: hasInternalIntervals,
+            hasExternalIntervals: hasExternalIntervals
+        };
+    };
+
+    // ---- axis tick mathematics -----------------------------------------
+    // The smallest 1/2/5 x 10^k (k may be negative) step >= target.
+    forester.niceAxisStep = function (target) {
+        if (!(target > 0) || !isFinite(target)) {
+            return 1;
+        }
+        let mag = Math.pow(10, Math.floor(Math.log(target) / Math.LN10));
+        let candidates = [1, 2, 5, 10];
+        for (let i = 0; i < candidates.length; ++i) {
+            let s = candidates[i] * mag;
+            if (s >= target - 1e-12) {
+                return s;
+            }
+        }
+        return 10 * mag;
+    };
+
+    // Tick ages for a "Ma before present" ruler: ~8 nice steps from 0 back
+    // to the root age.
+    forester.maAxisTickValues = function (rootAge) {
+        if (!(rootAge > 0) || !isFinite(rootAge)) {
+            return [];
+        }
+        let step = forester.niceAxisStep(rootAge / 8);
+        let vals = [];
+        for (let v = 0; v <= rootAge + 1e-9; v += step) {
+            vals.push(Math.round(v * 1e6) / 1e6);
+        }
+        return vals;
+    };
+
+    // Whole-year calendar ticks over [from, to]: nice 1/2/5 x 10^k integer
+    // steps, ~7 ticks.
+    forester.calendarTickYears = function (from, to) {
+        let span = to - from;
+        if (!(span > 0) || !isFinite(span) || !isFinite(from)) {
+            return [];
+        }
+        let step = Math.max(1, Math.round(forester.niceAxisStep(span / 7)));
+        let vals = [];
+        for (let y = Math.ceil(from / step) * step; y <= to + 1e-9; y += step) {
+            vals.push(y);
+        }
+        return vals;
+    };
+
+
+    // --------------------------------------------------------------
+    // Multiple sequence alignment (the desktop's alignment track)
+    // --------------------------------------------------------------
+    // Residue palettes, gap handling, conservation scoring and the hover
+    // readout data -- all pure, shared by the viewer's alignment track.
+    // Palettes are the desktop's (MsaColors.java): a Zappo-style 7-class
+    // physico-chemical scheme for amino acids, one colour per base for
+    // nucleotides, muted grey for ambiguity codes, and NO fill for a gap.
+
+    const MSA_GAP_CHARS = {'-': true, '.': true, ' ': true, '~': true};
+
+    // [r, g, b] triples so the letter-ink contrast rule can read them.
+    const MSA_AA_CLASSES = [
+        {residues: 'ILVAM', clazz: 'aliphatic (hydrophobic)', rgb: [240, 170, 170]},
+        {residues: 'FWY', clazz: 'aromatic', rgb: [240, 190, 90]},
+        {residues: 'KRH', clazz: 'positively charged', rgb: [120, 130, 240]},
+        {residues: 'DE', clazz: 'negatively charged', rgb: [230, 100, 100]},
+        {residues: 'STNQ', clazz: 'polar (hydrophilic)', rgb: [120, 200, 120]},
+        {residues: 'PG', clazz: 'conformationally special', rgb: [220, 130, 220]},
+        {residues: 'C', clazz: 'cysteine', rgb: [235, 220, 110]}
+    ];
+    const MSA_NT_RGB = {
+        A: [120, 200, 120],
+        C: [120, 130, 240],
+        G: [230, 185, 80],
+        T: [230, 110, 110],
+        U: [230, 110, 110]
+    };
+    const MSA_UNKNOWN_RGB = [205, 205, 205];
+
+    const MSA_AA_RGB = {};
+    const MSA_AA_CLASS = {};
+    MSA_AA_CLASSES.forEach(function (c) {
+        for (let i = 0; i < c.residues.length; ++i) {
+            MSA_AA_RGB[c.residues.charAt(i)] = c.rgb;
+            MSA_AA_CLASS[c.residues.charAt(i)] = c.clazz;
+        }
+    });
+    // The palette triples and the geologic table are handed out by reference;
+    // freezing them keeps one careless caller mutation from permanently
+    // recolouring a whole residue class (or renaming the Cretaceous).
+    MSA_AA_CLASSES.forEach(function (c) {
+        Object.freeze(c.rgb);
+    });
+    Object.keys(MSA_NT_RGB).forEach(function (k) {
+        Object.freeze(MSA_NT_RGB[k]);
+    });
+    Object.freeze(MSA_UNKNOWN_RGB);
+    Object.keys(GEO_SCALE).forEach(function (rank) {
+        GEO_SCALE[rank].forEach(Object.freeze);
+        Object.freeze(GEO_SCALE[rank]);
+    });
+
+    // Kyte-Doolittle hydropathy and full residue names, for the hover readout.
+    const MSA_HYDROPATHY = {
+        I: 4.5, V: 4.2, L: 3.8, F: 2.8, C: 2.5, M: 1.9, A: 1.8, G: -0.4,
+        T: -0.7, S: -0.8, W: -0.9, Y: -1.3, P: -1.6, H: -3.2, E: -3.5,
+        Q: -3.5, D: -3.5, N: -3.5, K: -3.9, R: -4.5
+    };
+    const MSA_AA_NAMES = {
+        A: 'Alanine', R: 'Arginine', N: 'Asparagine', D: 'Aspartic acid',
+        C: 'Cysteine', E: 'Glutamic acid', Q: 'Glutamine', G: 'Glycine',
+        H: 'Histidine', I: 'Isoleucine', L: 'Leucine', K: 'Lysine',
+        M: 'Methionine', F: 'Phenylalanine', P: 'Proline', S: 'Serine',
+        T: 'Threonine', W: 'Tryptophan', Y: 'Tyrosine', V: 'Valine',
+        U: 'Selenocysteine', O: 'Pyrrolysine',
+        B: 'Asparagine or aspartic acid', Z: 'Glutamine or glutamic acid',
+        X: 'Any amino acid', '*': 'stop'
+    };
+    const MSA_NT_NAMES = {
+        A: 'Adenine', C: 'Cytosine', G: 'Guanine', T: 'Thymine',
+        U: 'Uracil', N: 'any base'
+    };
+    const MSA_NT_CLASS = {
+        A: 'purine', G: 'purine', C: 'pyrimidine', T: 'pyrimidine', U: 'pyrimidine'
+    };
+
+    forester.isMsaGap = function (ch) {
+        return MSA_GAP_CHARS[ch] === true;
+    };
+
+    // The residue's fill as an [r,g,b] triple, or null for a gap (drawn as a
+    // faint dash, not a filled cell).
+    forester.msaResidueRgb = function (ch, nucleotide) {
+        if (ch === undefined || ch === null || forester.isMsaGap(ch)) {
+            return null;
+        }
+        let u = ch.toUpperCase();
+        let rgb = nucleotide ? MSA_NT_RGB[u] : MSA_AA_RGB[u];
+        return rgb ? rgb : MSA_UNKNOWN_RGB;
+    };
+
+    // Black or white letter ink over the given cell colour, by luminance --
+    // the same rule the desktop uses.
+    forester.msaLetterInk = function (rgb) {
+        if (!rgb) {
+            return '#404040'; // over a gap / unfilled cell, as on the desktop
+        }
+        let luminance = (0.299 * rgb[0]) + (0.587 * rgb[1]) + (0.114 * rgb[2]);
+        return luminance < 140 ? '#ffffff' : '#000000';
+    };
+
+    // Amino acid or nucleotide? Judged on the actual residues, never on any
+    // declared type: the fraction of non-gap characters that are plausible
+    // bases (ACGTUN) decides.
+    forester.msaIsNucleotide = function (seq) {
+        if (!seq) {
+            return false;
+        }
+        let bases = 0;
+        let residues = 0;
+        for (let i = 0; i < seq.length; ++i) {
+            let ch = seq.charAt(i);
+            if (forester.isMsaGap(ch)) {
+                continue;
+            }
+            ++residues;
+            if ('ACGTUNacgtun'.indexOf(ch) >= 0) {
+                ++bases;
+            }
+        }
+        return residues > 0 && (bases / residues) > 0.9;
+    };
+
+    // Per-column conservation over the given rows (gapped strings; a short
+    // row's missing tail counts as gaps). Two measures, both in [0,1]:
+    // 'identity' -- the fraction of ROWS carrying the column's most common
+    // residue (gaps stay in the denominator); 'information' -- the Schneider
+    // & Stephens sequence-logo information content, normalized by log2(K)
+    // (K = 4 or 20) and scaled by the column's non-gap fraction. Consensus is
+    // the most common NON-gap residue, ties broken alphabetically so figures
+    // are reproducible.
+    forester.msaConservation = function (rows, length, measure, nucleotide) {
+        if (!(length >= 0) || !isFinite(length)) {
+            return {scores: [], consensus: []};
+        }
+        length = Math.floor(length);
+        let n = rows.length;
+        let scores = new Array(length);
+        let consensus = new Array(length);
+        let K = nucleotide ? 4 : 20;
+        let log2K = Math.log(K) / Math.LN2;
+        for (let c = 0; c < length; ++c) {
+            let counts = {};
+            let nonGap = 0;
+            for (let r = 0; r < n; ++r) {
+                let row = rows[r];
+                let ch = (row && c < row.length) ? row.charAt(c) : '-';
+                if (forester.isMsaGap(ch)) {
+                    continue;
+                }
+                ch = ch.toUpperCase();
+                ++nonGap;
+                counts[ch] = (counts[ch] || 0) + 1;
+            }
+            let best = null;
+            let bestCount = 0;
+            Object.keys(counts).sort().forEach(function (ch) {
+                if (counts[ch] > bestCount) {
+                    bestCount = counts[ch];
+                    best = ch;
+                }
+            });
+            consensus[c] = best;
+            if (n < 1 || nonGap < 1) {
+                scores[c] = 0;
+            } else if (measure === 'information') {
+                let H = 0;
+                Object.keys(counts).forEach(function (ch) {
+                    let p = counts[ch] / nonGap;
+                    H -= p * (Math.log(p) / Math.LN2);
+                });
+                let info = (log2K - H) / log2K;
+                scores[c] = Math.max(0, info) * (nonGap / n);
+            } else {
+                scores[c] = bestCount / n;
+            }
+        }
+        return {scores: scores, consensus: consensus};
+    };
+
+    // The hover readout's description of one residue: full name, class (amino
+    // acids), Kyte-Doolittle hydropathy. Returns null for a gap.
+    forester.msaResidueInfo = function (ch, nucleotide) {
+        if (ch === undefined || ch === null || forester.isMsaGap(ch)) {
+            return null;
+        }
+        let u = ch.toUpperCase();
+        if (nucleotide) {
+            return {
+                name: MSA_NT_NAMES[u] || 'ambiguity code',
+                clazz: MSA_NT_CLASS[u] || null,
+                hydropathy: null
+            };
+        }
+        let clazz = MSA_AA_CLASS[u] || 'non-standard / ambiguity code';
+        if (u === 'C') {
+            clazz = 'cysteine (disulphide-forming)';
+        }
+        return {
+            name: MSA_AA_NAMES[u] || 'ambiguity code',
+            clazz: clazz,
+            hydropathy: (MSA_HYDROPATHY[u] !== undefined) ? MSA_HYDROPATHY[u] : null
+        };
+    };
+
+    // The residue's 1-based position within its own UNGAPPED sequence -- the
+    // coordinate that maps back onto the real molecule -- or null on a gap.
+    forester.msaUngappedPosition = function (row, col) {
+        if (!row || col < 0 || col >= row.length || forester.isMsaGap(row.charAt(col))) {
+            return null;
+        }
+        let pos = 0;
+        for (let i = 0; i <= col; ++i) {
+            if (!forester.isMsaGap(row.charAt(i))) {
+                ++pos;
+            }
+        }
+        return pos;
+    };
+
+
+    // --------------------------------------------------------------
+    // Unrooted (equal-angle) layout
+    // --------------------------------------------------------------
+    // The desktop's unrooted display: Meacham's equal-angle algorithm, one
+    // pass, no daylight iterations. The root sits at (0,0) and owns the full
+    // circle [startAngle, startAngle + 2*pi); each child receives a wedge of
+    // its parent's proportional to the external nodes it encloses and sits at
+    // its wedge's mid-angle, at the distance lengthOf(child) gives (branch
+    // length times the caller's scale factor, or a constant for a cladogram).
+    // Angles are ABSOLUTE screen angles (radians, y down), inherited and
+    // subdivided -- never re-referenced to the incoming branch, whose
+    // direction is implicitly each wedge's midpoint.
+    //
+    // Writes ux, uy (position) and uangle (the incoming spoke's screen angle)
+    // onto every node; returns {maxRad}, the largest distance from the root.
+    forester.equalAngleLayout = function (root, startAngle, lengthOf) {
+        let counts = new Map();
+        let countExt = function (n) {
+            let c;
+            if (!n.children || n.children.length < 1) {
+                c = 1;
+            } else {
+                c = 0;
+                for (let i = 0; i < n.children.length; ++i) {
+                    c += countExt(n.children[i]);
+                }
+            }
+            counts.set(n, c);
+            return c;
+        };
+        countExt(root);
+        let maxRad = 0;
+        root.ux = 0;
+        root.uy = 0;
+        root.uangle = startAngle;
+        let recurse = function (n, low, high) {
+            if (!n.children || n.children.length < 1) {
+                return;
+            }
+            let total = counts.get(n);
+            let current = low;
+            for (let i = 0; i < n.children.length; ++i) {
+                let desc = n.children[i];
+                let arc = (counts.get(desc) / total) * (high - low);
+                let mid = current + (arc / 2);
+                let len = lengthOf(desc);
+                desc.ux = n.ux + (Math.cos(mid) * len);
+                desc.uy = n.uy + (Math.sin(mid) * len);
+                desc.uangle = mid;
+                let r = Math.sqrt((desc.ux * desc.ux) + (desc.uy * desc.uy));
+                if (r > maxRad) {
+                    maxRad = r;
+                }
+                recurse(desc, current, current + arc);
+                current += arc;
+            }
+        };
+        recurse(root, startAngle, startAngle + (2 * Math.PI));
+        return {maxRad: maxRad};
+    };
+
+
+    // --------------------------------------------------------------
+    // Label-field suggestion
+    // --------------------------------------------------------------
+    // Decides which of the three label groups (node name, taxonomy, sequence)
+    // should START checked when a tree is loaded. Two rules, judged on the
+    // external nodes' actual label text (supplied by the caller's extractors,
+    // so the decision is made on exactly what would be printed):
+    //
+    // 1. Redundancy: a field whose text is CONTAINED in another checked
+    //    field's text (case-insensitively, ignoring spaces and underscores)
+    //    for at least 90% of the nodes carrying both adds nothing and starts
+    //    unchecked. On mutual containment the earlier field in the priority
+    //    order name > taxonomy > sequence is kept.
+    //
+    // 2. Length budget: if the median combined label of the remaining fields
+    //    still exceeds 50 characters, only the single most IDENTIFYING field
+    //    stays: the one with the highest ratio of distinct values to ALL
+    //    external nodes (a label's job is telling nodes apart -- and a field
+    //    carried by only a few tips cannot identify the rest, however unique
+    //    its few values are). Within a tie (0.05) the priority order wins,
+    //    unless a later field is SUBSTANTIALLY more economical (median length
+    //    under 60% of the leader's).
+    //
+    // A field with no values at all is never checked. This only decides the
+    // INITIAL state; the caller's UI stays free to override.
+    //
+    // extractors: {name, taxonomy, sequence}, each a function(externalNode)
+    // returning the text that field would contribute to the node's label, or
+    // null / '' when it contributes nothing.
+    /**
+     * Reads bare numeric internal node labels as confidence values -- the
+     * dialect nearly every tree writer emits (RAxML, IQ-TREE, FastTree, MEGA,
+     * BV-BRC) writes branch support as `)100:0.05`, which the New Hampshire
+     * grammar makes an internal node NAME.
+     *
+     * The rule is shared with the desktop Java Archaeopteryx; change it only
+     * together with that implementation.
+     *
+     * mode 'auto' (the default) is ALL-OR-NOTHING: every candidate label must
+     * look like support, so a tree of real clade names is never touched.
+     * mode 'confidence' is PER-NODE and unbounded: every numeric label is
+     * promoted whatever its value, which is how a user forces a mixed tree
+     * (some clade names, some support) or an out-of-range scale. mode 'label'
+     * does nothing -- the labels stay names.
+     *
+     * The ROOT is never promoted in any mode: a confidence belongs to the
+     * branch ABOVE a node and the root has none, so a numeric label there is
+     * almost always the tree's name -- `)99;` would otherwise lose it while
+     * `)MyTree;` kept it.
+     *
+     * Promotion MOVES: the label is cleared as the confidence is added, or the
+     * value would be drawn twice.
+     *
+     * Pure apart from the mutation it is asked to make, and returns the number
+     * of labels promoted so the CALLER can react (the viewer switches its
+     * confidence display on, so support values appear rather than names
+     * silently vanishing). Deliberately does not touch display state itself.
+     *
+     * @param phy - the phylogeny
+     * @param mode - 'auto' | 'confidence' | 'label'
+     * @returns {number} how many internal labels became confidences
+     */
+    forester.promoteInternalLabelsToConfidence = function (phy, mode) {
+        if (mode === 'label') {
+            return 0;
+        }
+        if (mode !== 'confidence') {
+            mode = 'auto';
+        }
+        let root = forester.getTreeRoot(phy);
+        let candidates = [];
+        let anyConfidence = false;
+        forester.preOrderTraversalAll(root, function (n) {
+            if (n === root || !(n.children || n._children)) {
+                return;
+            }
+            if (n.confidences && n.confidences.length > 0) {
+                anyConfidence = true;
+            }
+            if (typeof n.name === 'string' && n.name.length > 0) {
+                candidates.push(n);
+            }
+        });
+        if (candidates.length < 1) {
+            return 0;
+        }
+        let numeric = candidates.map(function (n) {
+            let v = Number(n.name);
+            return (n.name.trim().length > 0 && isFinite(v)) ? v : null;
+        });
+        let chosen;
+        if (mode === 'confidence') {
+            // Per node: promote what parses, leave the rest alone.
+            chosen = candidates.filter(function (n, i) {
+                return numeric[i] !== null;
+            });
+        } else {
+            // A file mixing `)[100]:` and `)95:` leaves the bracketed nodes
+            // with no label at all, so one bare numeric label beside real
+            // confidences is corroborated rather than lonely. Without this a
+            // mixed-dialect tree ships some confidences and one stray name.
+            let need = anyConfidence ? 1 : 2;
+            if (candidates.length < need) {
+                return 0;
+            }
+            if (numeric.some(function (v) {
+                // All-or-nothing: one real clade name and the tree is names.
+                // The range covers every scale in use -- 0-1 posteriors,
+                // 0-100 bootstrap, 0-1000 MrBayes -- and excludes identifiers
+                // such as NCBI taxids that would read as "support 9606".
+                return v === null || v < 0 || v > 1000;
+            })) {
+                return 0;
+            }
+            // Clade numbering is overwhelmingly 1..N, each exactly once. A
+            // real support tree containing every integer 1..N once and nothing
+            // else is essentially impossible at n >= 3, and without this guard
+            // a clade-numbered tree silently becomes "1%, 2%, 3% support".
+            let distinct = new Set(numeric);
+            let min = Math.min.apply(null, numeric);
+            let max = Math.max.apply(null, numeric);
+            if (distinct.size === numeric.length && min === 1 && max === numeric.length) {
+                return 0;
+            }
+            chosen = candidates;
+        }
+        chosen.forEach(function (n) {
+            let v = Number(n.name);
+            // Type deliberately left unset: the value cannot distinguish
+            // bootstrap from posterior from aLRT from TBE, and a wrong type
+            // printed beside a number in a published figure is worse than none.
+            pushConfidence(n, v, '');
+            n.name = '';
+        });
+        return chosen.length;
+    };
+
+    forester.suggestLabelFields = function (root, extractors) {
+        const FIELDS = ['name', 'taxonomy', 'sequence'];
+        const CONTAINMENT_MIN = 0.9;
+        const BUDGET_CHARS = 50;
+        const MIN_PAIRS = 2;
+        const TIE_EPSILON = 0.05;
+        const LENGTH_ADVANTAGE = 0.6;
+        let ext = forester.getAllExternalNodes(root);
+        let norm = function (s) {
+            return s.toLowerCase().replace(/[\s_]+/g, '');
+        };
+        let median = function (arr) {
+            if (arr.length < 1) {
+                return 0;
+            }
+            let a = arr.slice().sort(function (x, y) {
+                return x - y;
+            });
+            let m = a.length >> 1;
+            return (a.length % 2) ? a[m] : (a[m - 1] + a[m]) / 2;
+        };
+        let vals = {};
+        FIELDS.forEach(function (f) {
+            let get = extractors ? extractors[f] : null;
+            vals[f] = ext.map(function (n) {
+                let v = get ? get(n) : null;
+                v = (v === undefined || v === null) ? '' : String(v).trim();
+                return v.length > 0 ? v : null;
+            });
+        });
+        let stats = {};
+        FIELDS.forEach(function (f) {
+            let present = vals[f].filter(Boolean);
+            stats[f] = {
+                count: present.length,
+                medianLength: median(present.map(function (s) {
+                    return s.length;
+                })),
+                distinctRatio: (present.length > 0 && ext.length > 0)
+                    ? (new Set(present.map(norm)).size / ext.length) : 0
+            };
+        });
+        let checked = {};
+        FIELDS.forEach(function (f) {
+            checked[f] = stats[f].count > 0;
+        });
+
+        let containedFrac = function (inner, outer) {
+            let both = 0;
+            let contained = 0;
+            for (let i = 0; i < ext.length; ++i) {
+                let a = vals[outer][i];
+                let b = vals[inner][i];
+                if (a && b) {
+                    ++both;
+                    if (norm(a).indexOf(norm(b)) >= 0) {
+                        ++contained;
+                    }
+                }
+            }
+            return both >= MIN_PAIRS ? contained / both : 0;
+        };
+        for (let i = 0; i < FIELDS.length; ++i) {
+            for (let j = i + 1; j < FIELDS.length; ++j) {
+                let a = FIELDS[i];
+                let b = FIELDS[j];
+                if (!checked[a] || !checked[b]) {
+                    continue;
+                }
+                // on mutual containment this still drops b: a is earlier in
+                // the keep-priority order
+                if (containedFrac(b, a) >= CONTAINMENT_MIN) {
+                    checked[b] = false;
+                } else if (containedFrac(a, b) >= CONTAINMENT_MIN) {
+                    checked[a] = false;
+                }
+            }
+        }
+
+        let combined = [];
+        for (let i = 0; i < ext.length; ++i) {
+            let parts = [];
+            FIELDS.forEach(function (f) {
+                if (checked[f] && vals[f][i]) {
+                    parts.push(vals[f][i]);
+                }
+            });
+            if (parts.length > 0) {
+                combined.push(parts.join(' | ').length);
+            }
+        }
+        let medianCombined = median(combined);
+        let kept = FIELDS.filter(function (f) {
+            return checked[f];
+        });
+        if (medianCombined > BUDGET_CHARS && kept.length > 1) {
+            // top distinct-ratio first (a greedy pairwise chain is not
+            // transitive within the tie window); everything within the tie
+            // window then competes by priority order, with the economy rule
+            // as the only override
+            let maxDr = 0;
+            kept.forEach(function (f) {
+                if (stats[f].distinctRatio > maxDr) {
+                    maxDr = stats[f].distinctRatio;
+                }
+            });
+            let contenders = kept.filter(function (f) {
+                return stats[f].distinctRatio >= maxDr - TIE_EPSILON;
+            });
+            let best = contenders[0];
+            for (let k = 1; k < contenders.length; ++k) {
+                if (stats[contenders[k]].medianLength < LENGTH_ADVANTAGE * stats[best].medianLength) {
+                    best = contenders[k];
+                }
+            }
+            FIELDS.forEach(function (f) {
+                checked[f] = (f === best);
+            });
+        }
+        return {
+            showNodeName: checked.name,
+            showTaxonomy: checked.taxonomy,
+            showSequence: checked.sequence,
+            stats: {fields: stats, medianCombinedLength: medianCombined}
+        };
+    };
+
+
     // --------------------------------------------------------------
     // For exporting
     // --------------------------------------------------------------