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/dports/biology/iqtree/IQ-TREE-2.0.6/model/
H A Dpartitionmodel.cpp268 return tree_lh; in optimizeLinkedAlpha()
407 double tree_lh; in optimizeLinkedModels() local
448 double prev_tree_lh = -DBL_MAX, tree_lh = 0.0; in optimizeParameters() local
452 tree_lh = 0.0; in optimizeParameters()
468 tree_lh += score; in optimizeParameters()
495 ASSERT(new_tree_lh > tree_lh - 0.1); in optimizeParameters()
496 tree_lh = new_tree_lh; in optimizeParameters()
499 if (tree_lh-logl_epsilon*10 < prev_tree_lh) in optimizeParameters()
501 prev_tree_lh = tree_lh; in optimizeParameters()
511 return tree_lh; in optimizeParameters()
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H A Dpartitionmodelplen.cpp77 double tree_lh = 0.0, cur_lh = 0.0; in optimizeParameters() local
95 tree_lh = tree->computeLikelihood(); in optimizeParameters()
97 cout<<"Initial log-likelihood: "<<tree_lh<<endl; in optimizeParameters()
141 if (cur_lh <= tree_lh - 1.0) { in optimizeParameters()
146 ASSERT(cur_lh > tree_lh - 1.0 && "individual model opt reduces LnL"); in optimizeParameters()
156 ASSERT(cur_lh > tree_lh - 1.0 && "partition rate opt reduces LnL"); in optimizeParameters()
173 if(fabs(cur_lh-tree_lh) < logl_epsilon) { in optimizeParameters()
174 tree_lh = cur_lh; in optimizeParameters()
178 ASSERT(cur_lh > tree_lh - 1.0 && "branch length opt reduces LnL"); in optimizeParameters()
179 tree_lh = cur_lh; in optimizeParameters()
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H A Drateheterotachyinvar.cpp81 double tree_lh; in optimizeParameters() local
82 tree_lh = RateHeterotachy::optimizeParameters(gradient_epsilon); in optimizeParameters()
83 return tree_lh; in optimizeParameters()
H A Dratefreeinvar.cpp76 double tree_lh; in optimizeParameters() local
77 tree_lh = RateFree::optimizeParameters(gradient_epsilon); in optimizeParameters()
78 return tree_lh; in optimizeParameters()
H A Drateheterogeneity.h268 virtual double classifyRates(double tree_lh) { return tree_lh; } in classifyRates() argument
H A Dratemeyerdiscrete.h100 virtual double classifyRates(double tree_lh);
H A Dratemeyerdiscrete.cpp501 double RateMeyerDiscrete::classifyRates(double tree_lh) { in classifyRates() argument
502 if (is_categorized) return tree_lh; in classifyRates()
520 double lh_diff = 2*(tree_lh - new_tree_lh); in classifyRates()
H A Dratemeyerhaeseler.cpp360 double tree_lh = phylo_tree->computeLikelihood(); in optimizeParameters() local
384 if (new_tree_lh < tree_lh - 1e-5) { in optimizeParameters()
391 new_tree_lh = tree_lh; in optimizeParameters()
/dports/biology/iqtree/IQ-TREE-2.0.6/tree/
H A Dphylokernelsitemodel.cpp583 double tree_lh = node_branch->lh_scale_factor + dad_branch->lh_scale_factor; in computeSitemodelLikelihoodBranchEigen() local
600 #pragma omp parallel for reduction(+: tree_lh) private(ptn, i, c) schedule(static) in computeSitemodelLikelihoodBranchEigen()
624 tree_lh += lh_ptn * ptn_freq[ptn]; in computeSitemodelLikelihoodBranchEigen()
654 tree_lh += lh_ptn * ptn_freq[ptn]; in computeSitemodelLikelihoodBranchEigen()
658 if (isnan(tree_lh) || isinf(tree_lh)) { in computeSitemodelLikelihoodBranchEigen()
674 tree_lh = current_it->lh_scale_factor + current_it_back->lh_scale_factor; in computeSitemodelLikelihoodBranchEigen()
679 tree_lh += _pattern_lh[ptn] * ptn_freq[ptn]; in computeSitemodelLikelihoodBranchEigen()
683 ASSERT(!isnan(tree_lh) && !isinf(tree_lh)); in computeSitemodelLikelihoodBranchEigen()
685 return tree_lh; in computeSitemodelLikelihoodBranchEigen()
725 tree_lh += lh_ptn * ptn_freq[ptn]; in computeSitemodelLikelihoodFromBufferEigen()
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H A Dphylokernelnonrev.cpp623 double tree_lh = 0.0; in computeNonrevLikelihoodBranch() local
682 #pragma omp parallel for reduction(+: tree_lh, prob_const) private(ptn, i, c) schedule(static,1) nu… in computeNonrevLikelihoodBranch()
717 tree_lh += lh_ptn * ptn_freq[ptn]; in computeNonrevLikelihoodBranch()
768 tree_lh += lh_ptn * ptn_freq[ptn]; in computeNonrevLikelihoodBranch()
780 if (std::isnan(tree_lh) || std::isinf(tree_lh)) { in computeNonrevLikelihoodBranch()
797 tree_lh = 0.0; in computeNonrevLikelihoodBranch()
802 tree_lh += _pattern_lh[ptn] * ptn_freq[ptn]; in computeNonrevLikelihoodBranch()
823 tree_lh -= aln->getNSite()*prob_const; in computeNonrevLikelihoodBranch()
824 ASSERT(!std::isnan(tree_lh) && !std::isinf(tree_lh)); in computeNonrevLikelihoodBranch()
827 ASSERT(!std::isnan(tree_lh) && !std::isinf(tree_lh)); in computeNonrevLikelihoodBranch()
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H A Dphylosupertreeunlinked.cpp227 double tree_lh = 0.0; in doTreeSearch() local
244 … parallel for schedule(dynamic) num_threads(num_threads) if (num_threads > 1) reduction(+: tree_lh) in doTreeSearch()
251 tree_lh += score; in doTreeSearch()
270 if (tree_lh < curScore) in doTreeSearch()
271 cout << "BETTER TREE FOUND: " << tree_lh << endl; in doTreeSearch()
272 curScore = tree_lh; in doTreeSearch()
H A Dphylokernelsitemodel.h565 VectorClass tree_lh = 0.0; in computeSitemodelLikelihoodBranchEigenSIMD() local
619 tree_lh = mul_add(lh_ptn_sum, freq, tree_lh); in computeSitemodelLikelihoodBranchEigenSIMD()
626 tree_lh += tree_lh_thread; in computeSitemodelLikelihoodBranchEigenSIMD()
677 tree_lh = mul_add(lh_ptn_sum, freq, tree_lh); in computeSitemodelLikelihoodBranchEigenSIMD()
684 tree_lh += tree_lh_thread; in computeSitemodelLikelihoodBranchEigenSIMD()
692 …double tree_lh_final = horizontal_add(tree_lh) + node_branch->lh_scale_factor + dad_branch->lh_sca… in computeSitemodelLikelihoodBranchEigenSIMD()
742 VectorClass tree_lh = 0.0; in computeSitemodelLikelihoodFromBufferEigenSIMD() local
786 tree_lh = mul_add(lh_ptn_sum, freq, tree_lh); in computeSitemodelLikelihoodFromBufferEigenSIMD()
793 tree_lh += tree_lh_thread; in computeSitemodelLikelihoodFromBufferEigenSIMD()
798 …double tree_lh_final = horizontal_add(tree_lh) + current_it->lh_scale_factor + current_it_back->lh… in computeSitemodelLikelihoodFromBufferEigenSIMD()
H A Dphylokernelmixrate.h827 tree_lh += horizontal_add(lh_final); in computeMixrateLikelihoodBranchEigenSIMD()
828 ASSERT(!isnan(tree_lh) && !isinf(tree_lh)); in computeMixrateLikelihoodBranchEigenSIMD()
919 tree_lh += horizontal_add(lh_final); in computeMixrateLikelihoodBranchEigenSIMD()
920 ASSERT(!isnan(tree_lh) && !isinf(tree_lh)); in computeMixrateLikelihoodBranchEigenSIMD()
968 tree_lh -= aln->getNSite()*prob_const; in computeMixrateLikelihoodBranchEigenSIMD()
972 return tree_lh; in computeMixrateLikelihoodBranchEigenSIMD()
1052 tree_lh += horizontal_add(lh_final); in computeMixrateLikelihoodFromBufferEigenSIMD()
1053 if (isnan(tree_lh) || isinf(tree_lh)) { in computeMixrateLikelihoodFromBufferEigenSIMD()
1073 tree_lh += _pattern_lh[ptn] * ptn_freq[ptn]; in computeMixrateLikelihoodFromBufferEigenSIMD()
1137 tree_lh -= aln->getNSite() * prob_const; in computeMixrateLikelihoodFromBufferEigenSIMD()
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H A Dphylokernelmixture.h884 tree_lh += horizontal_add(lh_final); in computeMixtureLikelihoodBranchEigenSIMD()
885 if (isnan(tree_lh) || isinf(tree_lh)) { in computeMixtureLikelihoodBranchEigenSIMD()
1001 tree_lh += horizontal_add(lh_final); in computeMixtureLikelihoodBranchEigenSIMD()
1002 ASSERT(!isnan(tree_lh) && !isinf(tree_lh)); in computeMixtureLikelihoodBranchEigenSIMD()
1050 tree_lh -= aln->getNSite()*prob_const; in computeMixtureLikelihoodBranchEigenSIMD()
1054 return tree_lh; in computeMixtureLikelihoodBranchEigenSIMD()
1137 tree_lh += horizontal_add(lh_final); in computeMixtureLikelihoodFromBufferEigenSIMD()
1138 if (isnan(tree_lh) || isinf(tree_lh)) { in computeMixtureLikelihoodFromBufferEigenSIMD()
1158 tree_lh += _pattern_lh[ptn] * ptn_freq[ptn]; in computeMixtureLikelihoodFromBufferEigenSIMD()
1222 tree_lh -= aln->getNSite() * prob_const; in computeMixtureLikelihoodFromBufferEigenSIMD()
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H A Dphylotreemixlen.cpp243 double tree_lh = relative_rate->optimizeParameters(tolerance); in initializeMixlen() local
437 double tree_lh = -DBL_MAX; in optimizeOneBranch() local
443 if (new_tree_lh+1.0 < tree_lh) in optimizeOneBranch()
444 …M step " << EM_step << " new_tree_lh " << new_tree_lh << " worse than tree_lh " << tree_lh << endl; in optimizeOneBranch()
445 if (new_tree_lh-params->min_branch_length < tree_lh) in optimizeOneBranch()
447 tree_lh = new_tree_lh; in optimizeOneBranch()
568 double tree_lh = PhyloTree::optimizeAllBranches(my_iterations, tolerance, maxNRStep); in optimizeAllBranches() local
573 return tree_lh; in optimizeAllBranches()
H A Dphylokernelsafe.h876 double tree_lh = node_branch->lh_scale_factor + dad_branch->lh_scale_factor; in computeLikelihoodBranchEigenSIMD() local
1008 tree_lh += horizontal_add(lh_final); in computeLikelihoodBranchEigenSIMD()
1010 ASSERT(!isnan(tree_lh) & !isinf(tree_lh) && "Numerical underflow for SIMD lh-branch"); in computeLikelihoodBranchEigenSIMD()
1138 tree_lh += horizontal_add(lh_final); in computeLikelihoodBranchEigenSIMD()
1139 ASSERT(!isnan(tree_lh) && !isinf(tree_lh)); in computeLikelihoodBranchEigenSIMD()
1222 tree_lh -= aln->getNSite()*prob_const; in computeLikelihoodBranchEigenSIMD()
1226 return tree_lh; in computeLikelihoodBranchEigenSIMD()
1312 tree_lh += horizontal_add(lh_final) + buffer_scale_all; in computeLikelihoodFromBufferEigenSIMD()
1314 ASSERT(!isnan(tree_lh) && !isinf(tree_lh) && "Numerical underflow for SIMD lh-FromBuffer"); in computeLikelihoodFromBufferEigenSIMD()
1379 tree_lh -= aln->getNSite() * prob_const; in computeLikelihoodFromBufferEigenSIMD()
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H A Dphylokernelnew.h2626 double tree_lh = 0.0; in computeLikelihoodBranchSIMD() local
3035 tree_lh += horizontal_add(all_tree_lh); in computeLikelihoodBranchSIMD()
3040 if (!std::isfinite(tree_lh)) { in computeLikelihoodBranchSIMD()
3048 if (!std::isfinite(tree_lh)) { in computeLikelihoodBranchSIMD()
3049 tree_lh = 0.0; in computeLikelihoodBranchSIMD()
3098 ASSERT(std::isfinite(tree_lh)); in computeLikelihoodBranchSIMD()
3101 return tree_lh; in computeLikelihoodBranchSIMD()
3276 if (!std::isfinite(tree_lh)) { in computeLikelihoodFromBufferSIMD()
3277 tree_lh = 0.0; in computeLikelihoodFromBufferSIMD()
3326 ASSERT(std::isfinite(tree_lh)); in computeLikelihoodFromBufferSIMD()
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H A Dphylokernelnonrev.h1051 double tree_lh = 0.0; local
1403 tree_lh = horizontal_add(all_tree_lh);
1405 if (!std::isfinite(tree_lh)) {
1414 if (!std::isfinite(tree_lh)) {
1415 tree_lh = 0.0;
1420 tree_lh += _pattern_lh[ptn] * ptn_freq[ptn];
1436 tree_lh -= aln->getNSite()*prob_const;
1437 ASSERT(std::isfinite(tree_lh));
1440 return tree_lh;
H A Dphylosupertree.cpp690 double tree_lh = 0.0; in computeLikelihood() local
698 tree_lh += part_info[i].cur_score; in computeLikelihood()
704 #pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(num_threads > 1) in computeLikelihood()
709 tree_lh += part_info[i].cur_score; in computeLikelihood()
712 return tree_lh; in computeLikelihood()
761 double tree_lh = 0.0; in optimizeAllBranches() local
765 #pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(num_threads > 1) in optimizeAllBranches()
770 tree_lh += part_info[i].cur_score; in optimizeAllBranches()
776 return tree_lh; in optimizeAllBranches()
H A Dphylotree.cpp1714 if (tree_lh == 0.0) { in computeLogLVariance()
1716 tree_lh += pattern_lh[i] * pattern_freq[i]; in computeLogLVariance()
1718 double avg_site_lh = tree_lh / nsite; in computeLogLVariance()
2762 if (new_tree_lh < tree_lh - tolerance*0.1) { in optimizeAllBranches()
2766 << tree_lh << " -> " << new_tree_lh << endl; in optimizeAllBranches()
2777 if (fabs(new_tree_lh-tree_lh) > max_delta_lh) { in optimizeAllBranches()
2782 ASSERT(fabs(new_tree_lh-tree_lh) < max_delta_lh); in optimizeAllBranches()
2787 if (tree_lh <= new_tree_lh && new_tree_lh <= tree_lh + tolerance) { in optimizeAllBranches()
2791 tree_lh = new_tree_lh; in optimizeAllBranches()
2793 curScore = tree_lh; in optimizeAllBranches()
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H A Dphylosupertreeplen.cpp294 double tree_lh = 0.0; in computeFunction() local
309 #pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(num_threads > 1) in computeFunction()
321 tree_lh += part_info[part].cur_score; in computeFunction()
325 tree_lh += part_info[part].cur_score; in computeFunction()
328 return -tree_lh; in computeFunction()
/dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/
H A Dngs.h191 virtual double classifyRates(double tree_lh) { return tree_lh; } in classifyRates() argument
/dports/biology/iqtree/IQ-TREE-2.0.6/main/
H A Dtreetesting.cpp822 double tree_lh; in performAUTest() local
824 tree_lh = 0.0; in performAUTest()
826 tree_lh += pattern_lh[ptn] * boot_sample_dbl[ptn]; in performAUTest()
828 tree_lh = tree->dotProductDoubleCall(pattern_lh, boot_sample_dbl, nptn); in performAUTest()
831 tree_lh /= r[k]; in performAUTest()
834 if (tree_lh > max_lh) { in performAUTest()
836 max_lh = tree_lh; in performAUTest()
838 } else if (tree_lh > second_max_lh) in performAUTest()
839 second_max_lh = tree_lh; in performAUTest()
841 treelhs[(tid*nscales+k)*nboot + boot] = tree_lh; in performAUTest()
H A Dphylotesting.h337 void computeInformationScores(double tree_lh, int df, int ssize, double &AIC, double &AICc, double …
339 double computeInformationScore(double tree_lh, int df, int ssize, ModelTestCriterion mtc);
H A Dphylotesting.cpp425 void computeInformationScores(double tree_lh, int df, int ssize, double &AIC, double &AICc, double … in computeInformationScores() argument
426 AIC = -2 * tree_lh + 2 * df; in computeInformationScores()
428 BIC = -2 * tree_lh + df * log(ssize); in computeInformationScores()
431 double computeInformationScore(double tree_lh, int df, int ssize, ModelTestCriterion mtc) { in computeInformationScore() argument
433 computeInformationScores(tree_lh, df, ssize, AIC, AICc, BIC); in computeInformationScore()

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