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Merged
merged 7 commits into from
Jul 30, 2024
Merged

Version 2.3.6 #284

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e403efa
Fixed #261 issue of init model name that has to be in all caps for li…
thomaskf Jul 5, 2024
8891b7d
Fixed the issue when using linked exchangeabilities under the mixture…
thomaskf Jul 11, 2024
eb52e38
Fixed the issue #272 in writing best_model.nex file
thomaskf Jul 11, 2024
84a17aa
not outputting comma in bestmodel.nex
thomaskf Jul 15, 2024
d2056c5
Add a missing ";" by the end of the model definition inside GTRPMIX.n…
thomaskf Jul 25, 2024
d0d7732
update the version number
thomaskf Jul 26, 2024
6785082
Fixed the issue in writing best_model.nex file
thomaskf Jul 26, 2024
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2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -87,7 +87,7 @@ endif()
# The version number.
set (iqtree_VERSION_MAJOR 2)
set (iqtree_VERSION_MINOR 3)
set (iqtree_VERSION_PATCH ".5")
set (iqtree_VERSION_PATCH ".6")

option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)

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2 changes: 1 addition & 1 deletion main/phyloanalysis.cpp
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Expand Up @@ -323,7 +323,7 @@ void reportNexusFile(ostream &out, ModelSubst *m) {
double f = 1.0 / m->num_states;
for (i = 0; i < m->num_states; i++)
out << " " << f;
out << endl;
out << ";" << endl;
out.precision(4);
out << "end;" << endl;
}
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2 changes: 1 addition & 1 deletion model/modelmixture.cpp
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Expand Up @@ -2429,8 +2429,8 @@ void ModelMixture::setBounds(double *lower_bound, double *upper_bound, bool *bou
// only consider the first class as this is a linked substitution matrix
iterator it = begin();
auto freq = (*it)->freq_type;
int ndim = (*it)->getNDim();
(*it)->freq_type=FREQ_USER_DEFINED;
int ndim = (*it)->getNDim();
(*it)->setBounds(&lower_bound[dim], &upper_bound[dim], &bound_check[dim]);
(*it)->freq_type=freq;
//manually set these params for the restartParameters method; TODO: properly fix this -JD
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4 changes: 3 additions & 1 deletion model/modelprotein.cpp
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Expand Up @@ -995,7 +995,9 @@ void ModelProtein::init(const char *model_name, string model_params, StateFreqTy
} else {
// initialize rate matrix with a model (default: POISSON) -JD
nxs_model = models_block->findModel(Params::getInstance().gtr20_model);
ASSERT(nxs_model);
if (nxs_model == nullptr) {
outError("Unknown init model: " + Params::getInstance().gtr20_model);
}
readParametersString(nxs_model->description, false);
rescaleRates(rates, getNumRateEntries());
}
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5 changes: 4 additions & 1 deletion tree/phylosupertree.cpp
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@bqminh bqminh Jul 26, 2024

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I'm unsure if this this the right way, when you changed from:
out << saln->partitions[part]->sequence_type << ", ";
to
out << saln->partitions[part]->sequence_type;
why is printing comma removed?

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@thomaskf thomaskf Jul 26, 2024

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Hi @bqminh ,

I just modified the code so that the comma will be printed out only when both sequence_type and pos are not empty.

if (!saln->partitions[part]->sequence_type.empty() && !pos.empty()) {
       out << ", ";
}

Original file line number Diff line number Diff line change
Expand Up @@ -1535,9 +1535,12 @@ void PhyloSuperTree::printBestPartitionParams(const char *filename) {
if (!saln->partitions[part]->aln_file.empty()) out << saln->partitions[part]->aln_file << ": ";
/*if (saln->partitions[part]->seq_type == SEQ_CODON)
out << "CODON, ";*/
out << saln->partitions[part]->sequence_type << ", ";
out << saln->partitions[part]->sequence_type;
string pos = saln->partitions[part]->position_spec;
replace(pos.begin(), pos.end(), ',' , ' ');
if (!saln->partitions[part]->sequence_type.empty() && !pos.empty()) {
out << ", ";
}
out << pos << ";" << endl;
}
out << " charpartition mymodels =" << endl;
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3 changes: 2 additions & 1 deletion utils/tools.cpp
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Expand Up @@ -1689,8 +1689,9 @@ void parseArg(int argc, char *argv[], Params &params) {
if (strcmp(argv[cnt], "--gtr20-model") == 0 || strcmp(argv[cnt], "--init-exchange") == 0) {
cnt++;
if (cnt >= argc)
throw "Use --gtr20-model <POISSON/LG>";
throw "Use " + string(argv[cnt-1]) + " <protein model name>";
params.gtr20_model = argv[cnt];
transform(params.gtr20_model.begin(), params.gtr20_model.end(), params.gtr20_model.begin(), ::toupper);
continue;
}
if (strcmp(argv[cnt], "--guess-multiplier") == 0) {
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