Change the default minimum branch length for MAST model to 1e-4

iqtree · Feb 24, 2024 · 03ed4fd · 03ed4fd
1 parent 2d2f473
commit 03ed4fd
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Showing 2 changed files with 3 additions and 75 deletions.
diff --git a/tree/iqtreemix.cpp b/tree/iqtreemix.cpp
@@ -1589,7 +1589,7 @@ void IQTreeMix::setMinBranchLen(Params& params) {
         }
         */
     }
-    // cout << setprecision(7) << "Minimum branch length is set to " << params.min_branch_length << endl;
+    cout << setprecision(7) << "Minimum branch length is set to " << params.min_branch_length << endl;
 }
 
 /** set pointer of params variable */
@@ -1903,64 +1903,6 @@ void showDoubleArrayContent(string name, int dim, double* arr) {
     cout << endl;
 }
 
-/**
-    Estimate the average branch length for each tree
-    Based on this value to set the minimum value of branch length
- */
-void IQTreeMix::estimateAvgBrLen() {
-    size_t i,j,k;
-    int freq;
-    int* parsimony_scores;
-    double avgLen;
-    vector<int> sumParScores;
-
-    if (!parsi_computed) {
-        // compute parsimony scores for each tree along the patterns
-        // results are stored in the array patn_parsimony
-        computeParsimony();
-    }
-
-    estAvgBrlen.clear();
-    sumParScores.clear();
-    for (i=0; i<ntree; i++)
-        sumParScores.push_back(0);
-
-    k=0;
-    for (i=0; i<nptn; i++) {
-        freq = ptn_freq[i];
-        for (j=0; j<ntree; j++) {
-            sumParScores[j] += patn_parsimony[k] * freq;
-            k++;
-        }
-    }
-
-    /*
-    cout << "sum of parsimony scores along all sites for each tree: ";
-    for (i=0; i<ntree; i++) {
-        if (i>0)
-            cout << ",";
-        cout << sumParScores[i];
-    }
-    cout << endl;
-    */
-
-    for (i=0; i<ntree; i++) {
-        avgLen = (double) sumParScores[i] / getAlnNSite() / nbranch;
-        estAvgBrlen.push_back(avgLen);
-    }
-
-    /*
-    cout << "estimated avg branch lengths: ";
-    for (i=0; i<ntree; i++) {
-        if (i>0)
-            cout <<",";
-        cout << estAvgBrlen[i];
-    }
-    cout << endl;
-    */
-}
-
-
 /**
     Initialize the tree weights using parsimony scores
     Idea:
@@ -2265,14 +2207,6 @@ string IQTreeMix::optimizeModelParameters(bool printInfo, double logl_epsilon) {
     // set all the branches of the same group to their weighted average for initialization of the branch lengths
     checkBranchGrp();
 
-    // adjust the minimum branch length if params.min_branch_length > 0.1 * estimate_avg_branch_len
-    estimateAvgBrLen();
-    for (i = 0; i < ntree; i++) {
-        if (params->min_branch_length > 0.1 * estAvgBrlen[i])
-            params->min_branch_length = 0.1 * estAvgBrlen[i];
-    }
-    cout << setprecision(7) << "Minimum branch length is set to " << params->min_branch_length << endl;
-
     // show trees
     // cout << "Initial trees:" << endl;
     // showTree();

diff --git a/tree/iqtreemix.h b/tree/iqtreemix.h
@@ -22,8 +22,8 @@
 //#include "phylokernelnew.h"
 #include <vectorclass/vectorclass.h>
 
-// by default, the minimum branch length for MAST model is 0.001
-#define MAST_MIN_BRANCH_LEN 1e-3;
+// by default, the minimum branch length for MAST model is 0.0001
+#define MAST_MIN_BRANCH_LEN 1e-4;
 
 // for checking the scaling for the likelihood values
 #define TINY_SCALE_DIFF 0.5
@@ -188,12 +188,6 @@ class IQTreeMix : public IQTree, public vector<IQTree*> {
      */
     virtual int testNumThreads();
 
-    /**
-        Estimate the average branch length for each tree
-        Based on this value to set the minimum value of branch length
-     */
-    void estimateAvgBrLen();
-
     /**
      Initialize the tree weights using parsimony scores
      Idea: