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Fig a bug in MixtureFinder #164

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Merged
bqminh merged 4 commits into from
May 14, 2026
Merged

Fig a bug in MixtureFinder #164

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efa3857
Merge pull request #2 from iqtree/master
HuaiyanRen Sep 18, 2025
7d48a7a
Merge pull request #4 from iqtree/master
HuaiyanRen May 11, 2026
69000ac
correctly write best MixtureFinder model info (k-class) to checkpoint…
HuaiyanRen Jan 22, 2026
4d46105
remove unnecessary variables for overwriting checkpoint.
HuaiyanRen May 12, 2026
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32 changes: 16 additions & 16 deletions main/phylotesting.cpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/*
* phylotesting.cpp
* implementation of ModelFinder and PartitionFinder
* implementation of ModelFinder, PartitionFinder and MixtureFinder
* Created on: Aug 23, 2013
* Author: minh
*/
Expand Down Expand Up @@ -6599,7 +6599,8 @@ double runMixtureFinderMain(Params &params, IQTree* &iqtree, ModelCheckpoint &mo
string best_model_AIC, best_model_AICc, best_model_BIC;
double best_score_AIC, best_score_AICc, best_score_BIC;
// Store the information of (k-1)-class models. Once (k-1)-class is better then k-class, the (k-1)-class models will be printed out as the global best.
string best_model_pre_AIC, best_model_pre_AICc, best_model_pre_BIC, best_model_pre_list;
string best_model_AIC_pre, best_model_AICc_pre, best_model_BIC_pre, best_model_list_pre;

Checkpoint *checkpoint;
int ssize;
int curr_df;
Expand Down Expand Up @@ -6666,10 +6667,10 @@ double runMixtureFinderMain(Params &params, IQTree* &iqtree, ModelCheckpoint &mo

cout << endl << "Model: " << best_subst_name << best_rate_name << "; df: " << curr_df << "; loglike: " << curr_loglike << "; " << criteria_str << " score: " << curr_score << endl;

ASSERT(model_info.getString("best_model_AIC", best_model_pre_AIC));
ASSERT(model_info.getString("best_model_AICc", best_model_pre_AICc));
ASSERT(model_info.getString("best_model_BIC", best_model_pre_BIC));
ASSERT(model_info.getString("best_model_list_" + criteria_str, best_model_pre_list));
model_info.getString("best_model_AIC", best_model_AIC_pre);
model_info.getString("best_model_AICc", best_model_AICc_pre);
model_info.getString("best_model_BIC", best_model_BIC_pre);
model_info.getString("best_model_list_" + criteria_str, best_model_list_pre);

// Step 3: keep adding a new class until no further improvement
if (params.opt_qmix_criteria == 1) {
Expand Down Expand Up @@ -6701,18 +6702,17 @@ double runMixtureFinderMain(Params &params, IQTree* &iqtree, ModelCheckpoint &mo
curr_score = best_model.getScore();
model_str = best_subst_name;

ASSERT(model_info.getString("best_model_AIC", best_model_pre_AIC));
ASSERT(model_info.getString("best_model_AICc", best_model_pre_AICc));
ASSERT(model_info.getString("best_model_BIC", best_model_pre_BIC));
ASSERT(model_info.getString("best_model_list_" + criteria_str, best_model_pre_list));

model_info.getString("best_model_AIC", best_model_AIC_pre);
model_info.getString("best_model_AICc", best_model_AICc_pre);
model_info.getString("best_model_BIC", best_model_BIC_pre);
model_info.getString("best_model_list_" + criteria_str, best_model_list_pre);
}
} while (better_model && getClassNum(best_subst_name)+1 <= params.max_mix_cats);

model_info.put("best_model_list_" + criteria_str, best_model_pre_list);
model_info.put("best_model_AIC", best_model_pre_AIC);
model_info.put("best_model_AICc", best_model_pre_AICc);
model_info.put("best_model_BIC", best_model_pre_BIC);
model_info.put("best_model_AIC", best_model_AIC_pre);
model_info.put("best_model_AICc", best_model_AICc_pre);
model_info.put("best_model_BIC", best_model_BIC_pre);
model_info.put("best_model_list_" + criteria_str, best_model_list_pre);

best_subst_name = model_str;
if (params.optimize_from_given_params == false)
Expand Down Expand Up @@ -6765,7 +6765,7 @@ void runMixtureFinder(Params &params, IQTree* &iqtree, ModelCheckpoint &model_in
double best_loglike;

bool mix_finder_mode = (params.model_name == "MIX+MF" || params.model_name == "MIX+MFP" || params.model_name == "MF+MIX" || params.model_name == "MFP+MIX");

if (!mix_finder_mode)
return;

Expand Down
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