/dports/biology/iqtree/IQ-TREE-2.0.6/model/ |
H A D | partitionmodel.cpp | 268 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() [all …]
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H A D | partitionmodelplen.cpp | 77 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() [all …]
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H A D | rateheterotachyinvar.cpp | 81 double tree_lh; in optimizeParameters() local 82 tree_lh = RateHeterotachy::optimizeParameters(gradient_epsilon); in optimizeParameters() 83 return tree_lh; in optimizeParameters()
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H A D | ratefreeinvar.cpp | 76 double tree_lh; in optimizeParameters() local 77 tree_lh = RateFree::optimizeParameters(gradient_epsilon); in optimizeParameters() 78 return tree_lh; in optimizeParameters()
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H A D | rateheterogeneity.h | 268 virtual double classifyRates(double tree_lh) { return tree_lh; } in classifyRates() argument
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H A D | ratemeyerdiscrete.h | 100 virtual double classifyRates(double tree_lh);
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H A D | ratemeyerdiscrete.cpp | 501 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()
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H A D | ratemeyerhaeseler.cpp | 360 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()
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | phylokernelsitemodel.cpp | 583 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() [all …]
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H A D | phylokernelnonrev.cpp | 623 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() [all …]
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H A D | phylosupertreeunlinked.cpp | 227 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()
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H A D | phylokernelsitemodel.h | 565 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()
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H A D | phylokernelmixrate.h | 827 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() [all …]
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H A D | phylokernelmixture.h | 884 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() [all …]
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H A D | phylotreemixlen.cpp | 243 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()
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H A D | phylokernelsafe.h | 876 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() [all …]
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H A D | phylokernelnew.h | 2626 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() [all …]
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H A D | phylokernelnonrev.h | 1051 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;
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H A D | phylosupertree.cpp | 690 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()
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H A D | phylotree.cpp | 1714 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() [all …]
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H A D | phylosupertreeplen.cpp | 294 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()
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/dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/ |
H A D | ngs.h | 191 virtual double classifyRates(double tree_lh) { return tree_lh; } in classifyRates() argument
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/dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
H A D | treetesting.cpp | 822 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()
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H A D | phylotesting.h | 337 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);
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H A D | phylotesting.cpp | 425 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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