react-msaview 4.4.6 → 4.6.0

package/dist/neighborJoining.js

@@ -0,0 +1,839 @@
+// Neighbor Joining tree construction using BLOSUM62 distances
+// Based on Saitou & Nei (1987) "The neighbor-joining method"
+const BLOSUM62 = {
+    A: {
+        A: 4,
+        R: -1,
+        N: -2,
+        D: -2,
+        C: 0,
+        Q: -1,
+        E: -1,
+        G: 0,
+        H: -2,
+        I: -1,
+        L: -1,
+        K: -1,
+        M: -1,
+        F: -2,
+        P: -1,
+        S: 1,
+        T: 0,
+        W: -3,
+        Y: -2,
+        V: 0,
+        B: -2,
+        Z: -1,
+        X: 0,
+        '*': -4,
+    },
+    R: {
+        A: -1,
+        R: 5,
+        N: 0,
+        D: -2,
+        C: -3,
+        Q: 1,
+        E: 0,
+        G: -2,
+        H: 0,
+        I: -3,
+        L: -2,
+        K: 2,
+        M: -1,
+        F: -3,
+        P: -2,
+        S: -1,
+        T: -1,
+        W: -3,
+        Y: -2,
+        V: -3,
+        B: -1,
+        Z: 0,
+        X: -1,
+        '*': -4,
+    },
+    N: {
+        A: -2,
+        R: 0,
+        N: 6,
+        D: 1,
+        C: -3,
+        Q: 0,
+        E: 0,
+        G: 0,
+        H: 1,
+        I: -3,
+        L: -3,
+        K: 0,
+        M: -2,
+        F: -3,
+        P: -2,
+        S: 1,
+        T: 0,
+        W: -4,
+        Y: -2,
+        V: -3,
+        B: 3,
+        Z: 0,
+        X: -1,
+        '*': -4,
+    },
+    D: {
+        A: -2,
+        R: -2,
+        N: 1,
+        D: 6,
+        C: -3,
+        Q: 0,
+        E: 2,
+        G: -1,
+        H: -1,
+        I: -3,
+        L: -4,
+        K: -1,
+        M: -3,
+        F: -3,
+        P: -1,
+        S: 0,
+        T: -1,
+        W: -4,
+        Y: -3,
+        V: -3,
+        B: 4,
+        Z: 1,
+        X: -1,
+        '*': -4,
+    },
+    C: {
+        A: 0,
+        R: -3,
+        N: -3,
+        D: -3,
+        C: 9,
+        Q: -3,
+        E: -4,
+        G: -3,
+        H: -3,
+        I: -1,
+        L: -1,
+        K: -3,
+        M: -1,
+        F: -2,
+        P: -3,
+        S: -1,
+        T: -1,
+        W: -2,
+        Y: -2,
+        V: -1,
+        B: -3,
+        Z: -3,
+        X: -2,
+        '*': -4,
+    },
+    Q: {
+        A: -1,
+        R: 1,
+        N: 0,
+        D: 0,
+        C: -3,
+        Q: 5,
+        E: 2,
+        G: -2,
+        H: 0,
+        I: -3,
+        L: -2,
+        K: 1,
+        M: 0,
+        F: -3,
+        P: -1,
+        S: 0,
+        T: -1,
+        W: -2,
+        Y: -1,
+        V: -2,
+        B: 0,
+        Z: 3,
+        X: -1,
+        '*': -4,
+    },
+    E: {
+        A: -1,
+        R: 0,
+        N: 0,
+        D: 2,
+        C: -4,
+        Q: 2,
+        E: 5,
+        G: -2,
+        H: 0,
+        I: -3,
+        L: -3,
+        K: 1,
+        M: -2,
+        F: -3,
+        P: -1,
+        S: 0,
+        T: -1,
+        W: -3,
+        Y: -2,
+        V: -2,
+        B: 1,
+        Z: 4,
+        X: -1,
+        '*': -4,
+    },
+    G: {
+        A: 0,
+        R: -2,
+        N: 0,
+        D: -1,
+        C: -3,
+        Q: -2,
+        E: -2,
+        G: 6,
+        H: -2,
+        I: -4,
+        L: -4,
+        K: -2,
+        M: -3,
+        F: -3,
+        P: -2,
+        S: 0,
+        T: -2,
+        W: -2,
+        Y: -3,
+        V: -3,
+        B: -1,
+        Z: -2,
+        X: -1,
+        '*': -4,
+    },
+    H: {
+        A: -2,
+        R: 0,
+        N: 1,
+        D: -1,
+        C: -3,
+        Q: 0,
+        E: 0,
+        G: -2,
+        H: 8,
+        I: -3,
+        L: -3,
+        K: -1,
+        M: -2,
+        F: -1,
+        P: -2,
+        S: -1,
+        T: -2,
+        W: -2,
+        Y: 2,
+        V: -3,
+        B: 0,
+        Z: 0,
+        X: -1,
+        '*': -4,
+    },
+    I: {
+        A: -1,
+        R: -3,
+        N: -3,
+        D: -3,
+        C: -1,
+        Q: -3,
+        E: -3,
+        G: -4,
+        H: -3,
+        I: 4,
+        L: 2,
+        K: -3,
+        M: 1,
+        F: 0,
+        P: -3,
+        S: -2,
+        T: -1,
+        W: -3,
+        Y: -1,
+        V: 3,
+        B: -3,
+        Z: -3,
+        X: -1,
+        '*': -4,
+    },
+    L: {
+        A: -1,
+        R: -2,
+        N: -3,
+        D: -4,
+        C: -1,
+        Q: -2,
+        E: -3,
+        G: -4,
+        H: -3,
+        I: 2,
+        L: 4,
+        K: -2,
+        M: 2,
+        F: 0,
+        P: -3,
+        S: -2,
+        T: -1,
+        W: -2,
+        Y: -1,
+        V: 1,
+        B: -4,
+        Z: -3,
+        X: -1,
+        '*': -4,
+    },
+    K: {
+        A: -1,
+        R: 2,
+        N: 0,
+        D: -1,
+        C: -3,
+        Q: 1,
+        E: 1,
+        G: -2,
+        H: -1,
+        I: -3,
+        L: -2,
+        K: 5,
+        M: -1,
+        F: -3,
+        P: -1,
+        S: 0,
+        T: -1,
+        W: -3,
+        Y: -2,
+        V: -2,
+        B: 0,
+        Z: 1,
+        X: -1,
+        '*': -4,
+    },
+    M: {
+        A: -1,
+        R: -1,
+        N: -2,
+        D: -3,
+        C: -1,
+        Q: 0,
+        E: -2,
+        G: -3,
+        H: -2,
+        I: 1,
+        L: 2,
+        K: -1,
+        M: 5,
+        F: 0,
+        P: -2,
+        S: -1,
+        T: -1,
+        W: -1,
+        Y: -1,
+        V: 1,
+        B: -3,
+        Z: -1,
+        X: -1,
+        '*': -4,
+    },
+    F: {
+        A: -2,
+        R: -3,
+        N: -3,
+        D: -3,
+        C: -2,
+        Q: -3,
+        E: -3,
+        G: -3,
+        H: -1,
+        I: 0,
+        L: 0,
+        K: -3,
+        M: 0,
+        F: 6,
+        P: -4,
+        S: -2,
+        T: -2,
+        W: 1,
+        Y: 3,
+        V: -1,
+        B: -3,
+        Z: -3,
+        X: -1,
+        '*': -4,
+    },
+    P: {
+        A: -1,
+        R: -2,
+        N: -2,
+        D: -1,
+        C: -3,
+        Q: -1,
+        E: -1,
+        G: -2,
+        H: -2,
+        I: -3,
+        L: -3,
+        K: -1,
+        M: -2,
+        F: -4,
+        P: 7,
+        S: -1,
+        T: -1,
+        W: -4,
+        Y: -3,
+        V: -2,
+        B: -2,
+        Z: -1,
+        X: -2,
+        '*': -4,
+    },
+    S: {
+        A: 1,
+        R: -1,
+        N: 1,
+        D: 0,
+        C: -1,
+        Q: 0,
+        E: 0,
+        G: 0,
+        H: -1,
+        I: -2,
+        L: -2,
+        K: 0,
+        M: -1,
+        F: -2,
+        P: -1,
+        S: 4,
+        T: 1,
+        W: -3,
+        Y: -2,
+        V: -2,
+        B: 0,
+        Z: 0,
+        X: 0,
+        '*': -4,
+    },
+    T: {
+        A: 0,
+        R: -1,
+        N: 0,
+        D: -1,
+        C: -1,
+        Q: -1,
+        E: -1,
+        G: -2,
+        H: -2,
+        I: -1,
+        L: -1,
+        K: -1,
+        M: -1,
+        F: -2,
+        P: -1,
+        S: 1,
+        T: 5,
+        W: -2,
+        Y: -2,
+        V: 0,
+        B: -1,
+        Z: -1,
+        X: 0,
+        '*': -4,
+    },
+    W: {
+        A: -3,
+        R: -3,
+        N: -4,
+        D: -4,
+        C: -2,
+        Q: -2,
+        E: -3,
+        G: -2,
+        H: -2,
+        I: -3,
+        L: -2,
+        K: -3,
+        M: -1,
+        F: 1,
+        P: -4,
+        S: -3,
+        T: -2,
+        W: 11,
+        Y: 2,
+        V: -3,
+        B: -4,
+        Z: -3,
+        X: -2,
+        '*': -4,
+    },
+    Y: {
+        A: -2,
+        R: -2,
+        N: -2,
+        D: -3,
+        C: -2,
+        Q: -1,
+        E: -2,
+        G: -3,
+        H: 2,
+        I: -1,
+        L: -1,
+        K: -2,
+        M: -1,
+        F: 3,
+        P: -3,
+        S: -2,
+        T: -2,
+        W: 2,
+        Y: 7,
+        V: -1,
+        B: -3,
+        Z: -2,
+        X: -1,
+        '*': -4,
+    },
+    V: {
+        A: 0,
+        R: -3,
+        N: -3,
+        D: -3,
+        C: -1,
+        Q: -2,
+        E: -2,
+        G: -3,
+        H: -3,
+        I: 3,
+        L: 1,
+        K: -2,
+        M: 1,
+        F: -1,
+        P: -2,
+        S: -2,
+        T: 0,
+        W: -3,
+        Y: -1,
+        V: 4,
+        B: -3,
+        Z: -2,
+        X: -1,
+        '*': -4,
+    },
+    B: {
+        A: -2,
+        R: -1,
+        N: 3,
+        D: 4,
+        C: -3,
+        Q: 0,
+        E: 1,
+        G: -1,
+        H: 0,
+        I: -3,
+        L: -4,
+        K: 0,
+        M: -3,
+        F: -3,
+        P: -2,
+        S: 0,
+        T: -1,
+        W: -4,
+        Y: -3,
+        V: -3,
+        B: 4,
+        Z: 1,
+        X: -1,
+        '*': -4,
+    },
+    Z: {
+        A: -1,
+        R: 0,
+        N: 0,
+        D: 1,
+        C: -3,
+        Q: 3,
+        E: 4,
+        G: -2,
+        H: 0,
+        I: -3,
+        L: -3,
+        K: 1,
+        M: -1,
+        F: -3,
+        P: -1,
+        S: 0,
+        T: -1,
+        W: -3,
+        Y: -2,
+        V: -2,
+        B: 1,
+        Z: 4,
+        X: -1,
+        '*': -4,
+    },
+    X: {
+        A: 0,
+        R: -1,
+        N: -1,
+        D: -1,
+        C: -2,
+        Q: -1,
+        E: -1,
+        G: -1,
+        H: -1,
+        I: -1,
+        L: -1,
+        K: -1,
+        M: -1,
+        F: -1,
+        P: -2,
+        S: 0,
+        T: 0,
+        W: -2,
+        Y: -1,
+        V: -1,
+        B: -1,
+        Z: -1,
+        X: -1,
+        '*': -4,
+    },
+    '*': {
+        A: -4,
+        R: -4,
+        N: -4,
+        D: -4,
+        C: -4,
+        Q: -4,
+        E: -4,
+        G: -4,
+        H: -4,
+        I: -4,
+        L: -4,
+        K: -4,
+        M: -4,
+        F: -4,
+        P: -4,
+        S: -4,
+        T: -4,
+        W: -4,
+        Y: -4,
+        V: -4,
+        B: -4,
+        Z: -4,
+        X: -4,
+        '*': 1,
+    },
+};
+function getBlosum62Score(a, b) {
+    const upper_a = a.toUpperCase();
+    const upper_b = b.toUpperCase();
+    return BLOSUM62[upper_a]?.[upper_b] ?? -4;
+}
+function computePairwiseDistance(seq1, seq2) {
+    if (seq1.length !== seq2.length) {
+        throw new Error('Sequences must have the same length (aligned)');
+    }
+    let matches = 0;
+    let mismatches = 0;
+    let totalScore = 0;
+    let maxPossibleScore = 0;
+    for (let i = 0; i < seq1.length; i++) {
+        const a = seq1[i];
+        const b = seq2[i];
+        if (a === '-' && b === '-') {
+            continue;
+        }
+        if (a === '-' || b === '-') {
+            mismatches++;
+            continue;
+        }
+        const score = getBlosum62Score(a, b);
+        totalScore += score;
+        maxPossibleScore += Math.max(getBlosum62Score(a, a), getBlosum62Score(b, b));
+        if (a.toUpperCase() === b.toUpperCase()) {
+            matches++;
+        }
+        else {
+            mismatches++;
+        }
+    }
+    const total = matches + mismatches;
+    if (total === 0) {
+        return 1;
+    }
+    // Convert similarity to distance using normalized BLOSUM62 score
+    // Higher scores mean more similar, so we invert
+    if (maxPossibleScore <= 0) {
+        return 1;
+    }
+    const normalizedScore = totalScore / maxPossibleScore;
+    // Clamp to valid range and convert to distance
+    const clampedScore = Math.max(0.01, Math.min(1, normalizedScore));
+    // Use Kimura-like correction: d = -ln(similarity)
+    return -Math.log(clampedScore);
+}
+function computeDistanceMatrix(rows) {
+    const n = rows.length;
+    const distances = [];
+    for (let i = 0; i < n; i++) {
+        distances[i] = [];
+        for (let j = 0; j < n; j++) {
+            if (i === j) {
+                distances[i][j] = 0;
+            }
+            else if (j < i) {
+                distances[i][j] = distances[j][i];
+            }
+            else {
+                distances[i][j] = computePairwiseDistance(rows[i][1], rows[j][1]);
+            }
+        }
+    }
+    return distances;
+}
+function neighborJoining(distances, names) {
+    const n = distances.length;
+    if (n < 2) {
+        return { name: names[0] };
+    }
+    if (n === 2) {
+        const d = distances[0][1];
+        return {
+            left: { name: names[0] },
+            right: { name: names[1] },
+            leftLength: d / 2,
+            rightLength: d / 2,
+        };
+    }
+    // Work with copies that we'll modify
+    const D = [];
+    for (let i = 0; i < n; i++) {
+        D[i] = [...distances[i]];
+    }
+    const nodes = names.map(name => ({ name }));
+    let remaining = n;
+    while (remaining > 2) {
+        // Find active indices
+        const active = [];
+        for (let i = 0; i < nodes.length; i++) {
+            if (nodes[i] !== undefined) {
+                active.push(i);
+            }
+        }
+        // Compute r values (sum of distances for each node)
+        const r = new Map();
+        for (const i of active) {
+            let sum = 0;
+            for (const j of active) {
+                if (i !== j) {
+                    sum += D[i][j];
+                }
+            }
+            r.set(i, sum);
+        }
+        // Find pair with minimum Q value
+        let minQ = Infinity;
+        let minI = -1;
+        let minJ = -1;
+        for (let ai = 0; ai < active.length; ai++) {
+            for (let aj = ai + 1; aj < active.length; aj++) {
+                const i = active[ai];
+                const j = active[aj];
+                const q = (remaining - 2) * D[i][j] - r.get(i) - r.get(j);
+                if (q < minQ) {
+                    minQ = q;
+                    minI = i;
+                    minJ = j;
+                }
+            }
+        }
+        // Calculate branch lengths
+        const dij = D[minI][minJ];
+        const ri = r.get(minI);
+        const rj = r.get(minJ);
+        let limbI;
+        let limbJ;
+        if (remaining > 2) {
+            limbI = dij / 2 + (ri - rj) / (2 * (remaining - 2));
+            limbJ = dij - limbI;
+        }
+        else {
+            limbI = dij / 2;
+            limbJ = dij / 2;
+        }
+        // Ensure non-negative branch lengths
+        limbI = Math.max(0, limbI);
+        limbJ = Math.max(0, limbJ);
+        // Create new node
+        const newNode = {
+            left: nodes[minI],
+            right: nodes[minJ],
+            leftLength: limbI,
+            rightLength: limbJ,
+        };
+        // Update distance matrix
+        const newIdx = minI;
+        for (const k of active) {
+            if (k !== minI && k !== minJ) {
+                const newDist = (D[minI][k] + D[minJ][k] - dij) / 2;
+                D[newIdx][k] = Math.max(0, newDist);
+                D[k][newIdx] = Math.max(0, newDist);
+            }
+        }
+        // Mark minJ as removed
+        nodes[minJ] = undefined;
+        nodes[newIdx] = newNode;
+        remaining--;
+    }
+    // Connect final two nodes
+    const finalActive = [];
+    for (let i = 0; i < nodes.length; i++) {
+        if (nodes[i] !== undefined) {
+            finalActive.push(i);
+        }
+    }
+    if (finalActive.length === 2) {
+        const i = finalActive[0];
+        const j = finalActive[1];
+        const d = D[i][j];
+        return {
+            left: nodes[i],
+            right: nodes[j],
+            leftLength: d / 2,
+            rightLength: d / 2,
+        };
+    }
+    return nodes[finalActive[0]];
+}
+function nodeToNewick(node, branchLength) {
+    let result;
+    if (node.name !== undefined && !node.left && !node.right) {
+        // Leaf node - escape special characters in name
+        const escapedName = node.name.replace(/[():,;[\]]/g, '_');
+        result = escapedName;
+    }
+    else {
+        // Internal node
+        const leftNewick = node.left ? nodeToNewick(node.left, node.leftLength) : '';
+        const rightNewick = node.right
+            ? nodeToNewick(node.right, node.rightLength)
+            : '';
+        result = `(${leftNewick},${rightNewick})`;
+    }
+    if (branchLength !== undefined) {
+        result += `:${branchLength.toFixed(6)}`;
+    }
+    return result;
+}
+export function calculateNeighborJoiningTree(rows) {
+    if (rows.length < 2) {
+        throw new Error('Need at least 2 sequences to build a tree');
+    }
+    const names = rows.map(r => r[0]);
+    const distances = computeDistanceMatrix(rows);
+    const tree = neighborJoining(distances, names);
+    return nodeToNewick(tree) + ';';
+}
+//# sourceMappingURL=neighborJoining.js.map