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Searched refs:speciesTree (Results 1 – 4 of 4) sorted by relevance

/dports/biology/mrbayes/MrBayes-3.2.7/src/
H A Dbest.c243 if (speciesTree->bitsets == NULL) in GetDepthMatrix()
268 p = speciesTree->intDownPass[i]; in GetDepthMatrix()
306 if (speciesTree->bitsets == NULL) in GetMeanDist()
749 speciesTree = GetTree(m->speciesTree, chain, state[chain]); in LnSpeciesTreeProb()
873 p = &(speciesTree->nodes[i]); in LnPriorProbGeneTree()
927 GetDownPass(speciesTree); in LnPriorProbGeneTree()
931 FreeTreePartitions(speciesTree); in LnPriorProbGeneTree()
959 if (speciesTree->bitsets == NULL) in LnProposalProbSpeciesTree()
1058 …printf ("%-2d -- %d -- %d\n", speciesTree->allDownPass[i]->index, speciesTree->allDownPass[i]->x, … in MapGeneTreeToSpeciesTree()
1068 FreeTreePartitions(speciesTree); in MapGeneTreeToSpeciesTree()
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H A Dbest.h17 int IsSpeciesTreeConsistent (Tree *speciesTree, int chain);
19 double LnJointGeneTreeSpeciesTreePr (Tree **geneTrees, int numGeneTrees, Tree *speciesTree, int ch…
H A Dbayes.h1250 Param *speciesTree; /* ptr to species tree used in model */ member
H A Dmodel.c792 q = modelSettings[p->relParts[0]].speciesTree; in AllocateTreeParams()
10195 … theTree = GetTree (modelSettings[param->relParts[0]].speciesTree, chainId, 0); in DoStartvalsParm()
19335 modelSettings[i].speciesTree = p; in SetModelParams()
20032 Tree *speciesTree; in SetPopSizeParam() local
20042 speciesTree = GetTree (modelSettings[param->relParts[0]].speciesTree, chn, state); in SetPopSizeParam()
20046 AllocateTreePartitions(speciesTree); in SetPopSizeParam()
20050 for (j=0; j<speciesTree->nNodes-1; j++) in SetPopSizeParam()
20052 p = speciesTree->allDownPass[j]; in SetPopSizeParam()
20061 if (j == speciesTree->nNodes - 1) in SetPopSizeParam()
20065 FreeTreePartitions(speciesTree); in SetPopSizeParam()
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