/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylotreesse.cpp | 214 double PhyloTree::computeLikelihoodBranch(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeLikelihoodBranch() 219 void PhyloTree::computeLikelihoodDerv(PhyloNeighbor *dad_branch, PhyloNode *dad, double *df, double… in computeLikelihoodDerv() 1539 void PhyloTree::computeMarginalAncestralState(PhyloNeighbor *dad_branch, PhyloNode *dad, in computeMarginalAncestralState() 1783 void PhyloTree::computeAncestralLikelihood(PhyloNeighbor *dad_branch, PhyloNode *dad, int *C) { in computeAncestralLikelihood() 1963 void PhyloTree::computeAncestralState(PhyloNeighbor *dad_branch, PhyloNode *dad, int *C, int *ances… in computeAncestralState()
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H A D | phylokernel.h | 1465 void PhyloTree::computePartialParsimonyFastSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computePartialParsimonyFastSIMD() 1759 int PhyloTree::computeParsimonyBranchFastSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branc… in computeParsimonyBranchFastSIMD() 1846 void PhyloTree::computePartialParsimonySankoffSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad){ in computePartialParsimonySankoffSIMD() 2022 int PhyloTree::computeParsimonyBranchSankoffSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, int *br… in computeParsimonyBranchSankoffSIMD()
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H A D | phylotreepars.cpp | 32 void PhyloTree::computePartialParsimonyFast(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computePartialParsimonyFast() 241 int PhyloTree::computeParsimonyBranchFast(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branch_su… in computeParsimonyBranchFast() 350 PhyloNeighbor *dad_branch = (PhyloNeighbor*)nodes1[0]->findNeighbor(nodes2[0]); in setParsimonyBranchLengths() local 638 void PhyloTree::computePartialParsimonySankoff(PhyloNeighbor *dad_branch, PhyloNode *dad){ in computePartialParsimonySankoff() 793 int PhyloTree::computeParsimonyBranchSankoff(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branch… in computeParsimonyBranchSankoff()
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H A D | phylokernelnonrev.cpp | 18 PhyloNeighbor *dad_branch = info.dad_branch; in computeNonrevPartialLikelihood() local 370 void PhyloTree::computeNonrevLikelihoodDerv(PhyloNeighbor *dad_branch, PhyloNode *dad, double *df, … in computeNonrevLikelihoodDerv() 599 double PhyloTree::computeNonrevLikelihoodBranch(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeNonrevLikelihoodBranch()
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H A D | phylokernelsitemodel.cpp | 14 void PhyloTree::computeSitemodelPartialLikelihoodEigen(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeSitemodelPartialLikelihoodEigen() 443 void PhyloTree::computeSitemodelLikelihoodDervEigen(PhyloNeighbor *dad_branch, PhyloNode *dad, doub… in computeSitemodelLikelihoodDervEigen() 564 double PhyloTree::computeSitemodelLikelihoodBranchEigen(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeSitemodelLikelihoodBranchEigen()
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H A D | phylokernelsitemodel.h | 19 void PhyloTree::computeSitemodelPartialLikelihoodEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *da… in computeSitemodelPartialLikelihoodEigenSIMD() 375 void PhyloTree::computeSitemodelLikelihoodDervEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, … in computeSitemodelLikelihoodDervEigenSIMD() 539 double PhyloTree::computeSitemodelLikelihoodBranchEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *d… in computeSitemodelLikelihoodBranchEigenSIMD()
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H A D | phylokernelmixrate.h | 23 void PhyloTree::computeMixratePartialLikelihoodEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad)… in computeMixratePartialLikelihoodEigenSIMD() 452 void PhyloTree::computeMixrateLikelihoodDervEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, do… in computeMixrateLikelihoodDervEigenSIMD() 700 double PhyloTree::computeMixrateLikelihoodBranchEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad… in computeMixrateLikelihoodBranchEigenSIMD()
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H A D | phylokernelmixture.h | 21 void PhyloTree::computeMixturePartialLikelihoodEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad)… in computeMixturePartialLikelihoodEigenSIMD() 464 void PhyloTree::computeMixtureLikelihoodDervEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, do… in computeMixtureLikelihoodDervEigenSIMD() 730 double PhyloTree::computeMixtureLikelihoodBranchEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad… in computeMixtureLikelihoodBranchEigenSIMD()
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H A D | phylokernelsafe.h | 81 void PhyloTree::computePartialLikelihoodEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computePartialLikelihoodEigenSIMD() 567 void PhyloTree::computeLikelihoodDervEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, double &d… in computeLikelihoodDervEigenSIMD() 859 double PhyloTree::computeLikelihoodBranchEigenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeLikelihoodBranchEigenSIMD() 1460 void PhyloTree::computePartialParsimonyFastSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computePartialParsimonyFastSIMD() 1703 int PhyloTree::computeParsimonyBranchFastSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branc… in computeParsimonyBranchFastSIMD()
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H A D | phylokernelnonrev.h | 38 PhyloNeighbor *dad_branch = info.dad_branch; local 550 void PhyloTree::computeNonrevLikelihoodDervSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, double *… 1024 double PhyloTree::computeNonrevLikelihoodBranchSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) {
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H A D | phylotreemixlen.cpp | 322 void PhyloTreeMixlen::fixOneNegativeBranch(double branch_length, Neighbor *dad_branch, Node *dad) { in fixOneNegativeBranch() 745 PhyloNeighbor* dad_branch = current_it; in computeFuncDerv() local
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H A D | phylokernelnew.h | 1148 PhyloNeighbor *dad_branch = (PhyloNeighbor*)dad->findNeighbor(node); in computeTraversalInfo() local 1257 PhyloNeighbor *dad_branch = info.dad_branch; in computePartialLikelihoodSIMD() local 1984 void PhyloTree::computeLikelihoodBufferSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, size_t ptn_l… in computeLikelihoodBufferSIMD() 2155 void PhyloTree::computeLikelihoodDervSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, double *df, do… in computeLikelihoodDervSIMD() 2597 double PhyloTree::computeLikelihoodBranchSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad) in computeLikelihoodBranchSIMD() 3335 void PhyloTree::computeLikelihoodDervMixlenSIMD(PhyloNeighbor *dad_branch, PhyloNode *dad, double &… in computeLikelihoodDervMixlenSIMD()
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H A D | phylotree.cpp | 797 void PhyloTree::computePartialParsimony(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computePartialParsimony() 812 int PhyloTree::computeParsimonyBranch(PhyloNeighbor *dad_branch, PhyloNode *dad, int *branch_subst)… in computeParsimonyBranch() 2297 double PhyloTree::computeBayesianBranchLength(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeBayesianBranchLength() 2410 double PhyloTree::computeCorrectedBayesianBranchLength(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeCorrectedBayesianBranchLength() 2430 double PhyloTree::computeLikelihoodZeroBranch(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeLikelihoodZeroBranch() 3299 void PhyloTree::fixOneNegativeBranch(double branch_length, Neighbor *dad_branch, Node *dad) { in fixOneNegativeBranch() 5391 void PhyloTree::reorientPartialLh(PhyloNeighbor* dad_branch, Node *dad) { in reorientPartialLh() 5411 bool PhyloTree::computeTraversalInfo(PhyloNeighbor *dad_branch, PhyloNode *dad, double* &buffer) { in computeTraversalInfo()
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H A D | phylosupertreeplen.cpp | 331 double PhyloSuperTreePlen::computeLikelihoodBranch(PhyloNeighbor *dad_branch, PhyloNode *dad) { in computeLikelihoodBranch() 1855 void PhyloSuperTreePlen::reorientPartialLh(PhyloNeighbor* dad_branch, Node *dad) { in reorientPartialLh()
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H A D | phylosupertree.cpp | 620 int PhyloSuperTree::computeParsimonyBranchObsolete(PhyloNeighbor *dad_branch, PhyloNode *dad, int *… in computeParsimonyBranchObsolete() 1352 void PhyloSuperTree::computeMarginalAncestralState(PhyloNeighbor *dad_branch, PhyloNode *dad, in computeMarginalAncestralState()
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H A D | phylotree.h | 305 TraversalInfo(PhyloNeighbor *dad_branch, PhyloNode *dad) { in TraversalInfo()
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