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Fix EM mixture-frequency optimization #175

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Merged
bqminh merged 1 commit into from
Jun 18, 2026
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Fix EM mixture-frequency optimization #175

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2 changes: 2 additions & 0 deletions model/modelmixture.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4177,6 +4177,7 @@ double ModelMixture::optimizeWithEM(double gradient_epsilon) {
// EM algorithm loop described in Wang, Li, Susko, and Roger (2008)
for (step = 0; step < optimize_steps; step++) {
// first compute _pattern_lh_cat
phylo_tree->clearAllPartialLH();
score = phylo_tree->computePatternLhCat(WSL_MIXTURE);

if (score < prev_score + gradient_epsilon)
Expand Down Expand Up @@ -4254,6 +4255,7 @@ double ModelMixture::optimizeWithEM(double gradient_epsilon) {

if (c>0 && !Params::getInstance().optimize_linked_gtr) {
// compute _pattern_lh_cat
phylo_tree->clearAllPartialLH();
phylo_tree->computePatternLhCat(WSL_MIXTURE);
// update the posterior probabilities of each category
for (ptn = 0; ptn < nptn; ptn++) {
Expand Down
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