phykit 2.1.47__tar.gz → 2.1.49__tar.gz

{phykit-2.1.47 → phykit-2.1.49}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.47
+Version: 2.1.49
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -14,6 +14,22 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
+Requires-Dist: biopython>=1.82
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: umap-learn>=0.5.0
+Requires-Dist: tqdm>=4.65.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">

{phykit-2.1.47 → phykit-2.1.49}/phykit/helpers/plot_config.py

@@ -23,6 +23,7 @@ class PlotConfig:
     title_fontsize: Optional[float] = None
     axis_fontsize: Optional[float] = None
     colors: Optional[List[str]] = None
+    ladderize: bool = False
 
     def validate(self) -> None:
         if self.fig_width is not None and self.fig_width <= 0:
@@ -187,6 +188,7 @@ class PlotConfig:
             title_fontsize=getattr(args, "title_fontsize", None),
             axis_fontsize=getattr(args, "axis_fontsize", None),
             colors=colors,
+            ladderize=getattr(args, "ladderize", False),
         )
         config.validate()
         return config
@@ -205,3 +207,4 @@ def add_plot_arguments(parser) -> None:
     group.add_argument("--title-fontsize", type=float, default=None, help="Font size for the title")
     group.add_argument("--axis-fontsize", type=float, default=None, help="Font size for axis labels")
     group.add_argument("--colors", type=str, default=None, help="Comma-separated colors (hex or named)")
+    group.add_argument("--ladderize", action="store_true", default=False, help="Ladderize (sort) the tree before plotting")

{phykit-2.1.47 → phykit-2.1.49}/phykit/helpers/quartet_utils.py

@@ -2,8 +2,8 @@
 Shared utilities for quartet concordance factor computation and ASTRAL parsing.
 
 Provides gene concordance factor (gCF/gDF1/gDF2) computation via the
-four-group bipartition decomposition, and parsing of ASTRAL -t 2
-q1/q2/q3 annotations from Newick node labels.
+four-group bipartition decomposition, and parsing of ASTRAL -t 2 or
+wASTRAL --support 3 q1/q2/q3 annotations from Newick node labels.
 """
 from typing import Dict, List, Optional, Tuple
 
@@ -93,10 +93,11 @@ def compute_gcf_per_node(
 def parse_astral_annotations(
     tree,
 ) -> Dict[int, Tuple[float, float, float]]:
-    """Parse q1/q2/q3 annotations from ASTRAL -t 2 Newick node labels.
+    """Parse q1/q2/q3 annotations from ASTRAL/wASTRAL Newick node labels.
 
-    ASTRAL annotates internal nodes with formats like:
+    Supports ASTRAL -t 2 and wASTRAL --support 3 output formats:
       '[q1=0.5;q2=0.3;q3=0.2;f1=50;...]'
+      '[CULength=2.6;f1=108;...;q1=0.96;q2=0.03;q3=0.01]'
       'q1=0.5;q2=0.3;q3=0.2'
 
     Returns dict mapping clade id -> (q1, q2, q3).

{phykit-2.1.47 → phykit-2.1.49}/phykit/phykit.py

@@ -464,7 +464,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -512,6 +512,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -816,7 +819,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -862,6 +865,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -947,7 +953,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -992,6 +998,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1298,7 +1307,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1348,6 +1357,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1485,7 +1497,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1530,6 +1542,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -1831,7 +1846,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -1888,6 +1903,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -1961,7 +1979,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -2019,6 +2037,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -2249,7 +2270,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -2307,6 +2328,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -2920,7 +2944,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3006,6 +3030,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3255,7 +3282,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3307,6 +3334,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3606,7 +3636,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3661,6 +3691,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -3731,7 +3764,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3774,6 +3807,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to also
                                             output results as JSON
                 """
@@ -3823,7 +3859,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3876,6 +3912,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to also
                                             output results as JSON
                 """
@@ -3930,7 +3969,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -3973,6 +4012,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4019,7 +4061,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -4065,6 +4107,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4118,7 +4163,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -4170,6 +4215,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -4651,7 +4699,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -4702,6 +4750,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                     optional argument to output
                                            results as JSON
                 """
@@ -4747,7 +4798,8 @@ class Phykit:
                 In native mode (-g provided), computes gene concordance
                 factors (gCF, gDF1, gDF2) from a species tree and gene
                 trees via bipartition matching. In ASTRAL mode (no -g),
-                parses q1/q2/q3 annotations from ASTRAL -t 2 output.
+                parses q1/q2/q3 annotations from ASTRAL -t 2 output or
+                wASTRAL --support 3 output.
 
                 Pie slices show: concordant (blue), discordant alt 1
                 (red), discordant alt 2 (gray).
@@ -4765,7 +4817,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
 
                 Options
                 =====================================================
@@ -4773,7 +4825,8 @@ class Phykit:
 
                 -g/--gene-trees             gene trees file, one Newick
                                             tree per line (optional;
-                                            if omitted, ASTRAL -t 2
+                                            if omitted, ASTRAL -t 2 or
+                                            wASTRAL --support 3
                                             annotations are parsed)
 
                 -o/--output                 output figure path (required;
@@ -4813,6 +4866,9 @@ class Phykit:
                                             (default: "#2b8cbe,#d62728,
                                             #969696")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             per-node concordance as JSON
                 """
@@ -4877,7 +4933,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -4934,6 +4990,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                     optional argument to output
                                            results as JSON
                 """
@@ -5094,7 +5153,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -5140,6 +5199,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5248,7 +5310,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -5296,6 +5358,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5355,7 +5420,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -5419,6 +5484,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -5818,7 +5886,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -5875,6 +5943,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6054,7 +6125,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -6105,6 +6176,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6223,7 +6297,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -6268,6 +6342,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6323,7 +6400,7 @@ class Phykit:
                     [--legend-position <str>]
                     [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                     [--title-fontsize <float>] [--axis-fontsize <float>]
-                    [--colors <str>]
+                    [--colors <str>] [--ladderize]
                     [--json]
 
                 Options
@@ -6367,6 +6444,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """
@@ -6423,7 +6503,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
                   [--json]
 
                 Options
@@ -6481,6 +6561,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      output results as JSON
                 """
             ),
@@ -6554,7 +6637,7 @@ class Phykit:
                   [--legend-position <str>]
                   [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
                   [--title-fontsize <float>] [--axis-fontsize <float>]
-                  [--colors <str>]
+                  [--colors <str>] [--ladderize]
 
                 Options
                 =====================================================
@@ -6614,6 +6697,9 @@ class Phykit:
                                             (hex or named, e.g.,
                                             "#ff0000,blue,#00ff00")
 
+                --ladderize                 ladderize (sort) the tree
+                                            before plotting
+
                 --json                      optional argument to output
                                             results as JSON
                 """

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/ancestral_reconstruction.py

@@ -66,6 +66,9 @@ class AncestralReconstruction(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 
@@ -1206,6 +1209,9 @@ class AncestralReconstruction(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/concordance_asr.py

@@ -101,6 +101,9 @@ class ConcordanceAsr(Tree):
                 species_copy, tips_to_prune
             )
 
+        if self.plot_config.ladderize:
+            species_copy.ladderize()
+
         if self.method == "distribution":
             result = self._run_distribution(
                 species_copy, gene_trees, trait_values, all_taxa

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/cont_map.py

@@ -40,6 +40,9 @@ class ContMap(Tree):
         if tips_to_prune:
             tree_copy = self.prune_tree_using_taxa_list(tree_copy, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree_copy.ladderize()
+
         # Label internal nodes
         node_labels = self._label_internal_nodes(tree_copy)
 

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/cophylo.py

@@ -84,6 +84,10 @@ class Cophylo(Tree):
         n_tips1 = len(tips1)
         n_tips2 = len(tips2)
 
+        if self.plot_config.ladderize:
+            tree1.ladderize()
+            tree2.ladderize()
+
         # Optimize tip ordering to reduce line crossings
         tree1_order, tree2_order = self._optimize_tip_order(
             tree1, tree2, mapping_valid

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/density_map.py

@@ -64,6 +64,9 @@ class DensityMap(Tree):
             for tip_name in tips_to_prune:
                 tree.prune(tip_name)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Fit Q matrix using ER model
         Q, loglik = scm._fit_q_matrix(tree, tip_states, states, "ER")
         k = len(states)

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/discordance_asymmetry.py

@@ -85,6 +85,8 @@ class DiscordanceAsymmetry(Tree):
             self._output_text(branch_results, summary)
 
         if self.plot_output:
+            if self.plot_config.ladderize:
+                species_tree.ladderize()
             self._plot(species_tree, branch_results, self.plot_output,
                        shared_taxa=shared_taxa)
 

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/phylo_heatmap.py

@@ -43,6 +43,9 @@ class PhyloHeatmap(Tree):
         if tips_to_prune:
             tree = self.prune_tree_using_taxa_list(tree, tips_to_prune)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Get tip order from tree traversal
         tip_order = [t.name for t in tree.get_terminals()]
 

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/quartet_pie.py

@@ -5,7 +5,7 @@ Draws a phylogram with pie charts at internal nodes showing the
 proportion of gene trees supporting the species tree topology (gCF)
 versus the two NNI alternative topologies (gDF1, gDF2). Supports
 both native computation from gene trees and parsing of ASTRAL -t 2
-annotations.
+or wASTRAL --support 3 annotations.
 """
 import sys
 from typing import Dict, List, Tuple
@@ -50,7 +50,8 @@ class QuartetPie(Tree):
                     [
                         "No ASTRAL q1/q2/q3 annotations found in the tree.",
                         "Either provide gene trees with -g, or use an ASTRAL",
-                        "-t 2 output tree with quartet annotations.",
+                        "-t 2 or wASTRAL --support 3 output tree with quartet",
+                        "annotations.",
                     ],
                     code=2,
                 )
@@ -62,6 +63,9 @@ class QuartetPie(Tree):
             input_mode = "astral"
             n_gene_trees = 0
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         self._plot_quartet_pie(tree, proportions, self.output_path)
 
         if self.json_output:

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/rate_heterogeneity.py

@@ -108,6 +108,9 @@ class RateHeterogeneity(Tree):
 
         # Plot
         if self.plot_output:
+            if self.plot_config.ladderize:
+                tree_copy.ladderize()
+                parent_map = self._build_parent_map(tree_copy)
             self._plot_regime_tree(
                 tree_copy, branch_regimes, regimes, parent_map, self.plot_output
             )

{phykit-2.1.47 → phykit-2.1.49}/phykit/services/tree/stochastic_character_map.py

@@ -67,6 +67,9 @@ class StochasticCharacterMap(Tree):
             for tip_name in tips_to_prune:
                 tree.prune(tip_name)
 
+        if self.plot_config.ladderize:
+            tree.ladderize()
+
         # Fit Q matrix
         Q, loglik = self._fit_q_matrix(tree, tip_states, states, self.model)
         k = len(states)

phykit-2.1.49/phykit/version.py

@@ -0,0 +1 @@
+__version__ = "2.1.49"

{phykit-2.1.47 → phykit-2.1.49}/phykit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: phykit
-Version: 2.1.47
+Version: 2.1.49
 Home-page: https://github.com/jlsteenwyk/phykit
 Author: Jacob L. Steenwyk
 Author-email: jlsteenwyk@gmail.com
@@ -14,6 +14,22 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
+Requires-Dist: biopython>=1.82
+Requires-Dist: matplotlib>=3.7.0
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: scipy>=1.11.3
+Requires-Dist: scikit-learn>=1.4.2
+Requires-Dist: umap-learn>=0.5.0
+Requires-Dist: tqdm>=4.65.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
 
 <p align="center">
   <a href="https://github.com/jlsteenwyk/phykit">

phykit-2.1.47/phykit/version.py

@@ -1 +0,0 @@
-__version__ = "2.1.47"