/dports/biology/phyml/phyml-3.3.20200621/src/ |
H A D | tbe.c | 37 if(boot_tree->a_edges[j]->rght->tax) in Update_IC_Ref_Tree() 38 tip = boot_tree->a_edges[j]->rght; in Update_IC_Ref_Tree() 40 tip = boot_tree->a_edges[j]->left; in Update_IC_Ref_Tree() 63 if(boot_tree->a_edges[j]->rght->tax || boot_tree->a_edges[j]->left->tax){ in Update_IC_Ref_Tree() 78 if(!(boot_tree->a_edges[j]->rght->tax) && !(boot_tree->a_edges[j]->left->tax)) continue; in Update_IC_Ref_Tree() 173 if(!boot_tree->n_root){ in Update_All_IC_Boot_Tree() 175 while((!boot_tree->a_nodes[boot_tree->n_otu+i]->v[0]) || in Update_All_IC_Boot_Tree() 176 (!boot_tree->a_nodes[boot_tree->n_otu+i]->v[1]) || in Update_All_IC_Boot_Tree() 177 (!boot_tree->a_nodes[boot_tree->n_otu+i]->v[2])) i++; in Update_All_IC_Boot_Tree() 178 root=boot_tree->a_nodes[boot_tree->n_otu+i]; in Update_All_IC_Boot_Tree() [all …]
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H A D | mpi_boot.c | 30 t_tree *boot_tree; in Bootstrap_MPI() local 50 boot_tree = NULL; in Bootstrap_MPI() 228 boot_tree->n_pattern = boot_tree->data->crunch_len; in Bootstrap_MPI() 234 …if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE))… in Bootstrap_MPI() 236 Connect_CSeqs_To_Nodes(boot_data,boot_tree->io,boot_tree); in Bootstrap_MPI() 249 Lk(NULL,boot_tree); in Bootstrap_MPI() 258 if(boot_tree->mod->s_opt->opt_subst_param || boot_tree->mod->s_opt->opt_bl) in Bootstrap_MPI() 264 Free_Bip(boot_tree); in Bootstrap_MPI() 266 Alloc_Bip(boot_tree); in Bootstrap_MPI() 272 boot_tree); in Bootstrap_MPI() [all …]
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H A D | tbe.h | 19 void Update_All_IC_Ref_Tree(t_tree* ref_tree, t_tree* boot_tree, 21 …date_IC_Ref_Tree(t_tree *ref_tree, t_node * orig, t_node* target, t_edge *my_br, t_tree *boot_tree, 23 void Update_IC_Boot_Tree(t_tree* ref_tree, t_tree* boot_tree, t_node* orig, t_node* target, 27 void Update_All_IC_Boot_Tree(t_tree* ref_tree, t_tree* boot_tree,
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H A D | utilities.c | 3118 t_tree *boot_tree; in Bootstrap() local 3134 boot_tree = NULL; in Bootstrap() 3212 boot_tree->n_pattern = boot_tree->data->crunch_len; in Bootstrap() 3221 …if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE))… in Bootstrap() 3233 Update_Dirs(boot_tree); in Bootstrap() 3248 Lk(NULL,boot_tree); in Bootstrap() 3257 if(boot_tree->mod->s_opt->opt_subst_param || boot_tree->mod->s_opt->opt_bl) in Bootstrap() 3263 Free_Bip(boot_tree); in Bootstrap() 3264 Alloc_Bip(boot_tree); in Bootstrap() 3268 boot_tree); in Bootstrap() [all …]
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/dports/biology/seaview/seaview/ |
H A D | tbe.cxx | 155 for (j=0; j < 2*boot_tree->notu-2; j++) { /* for all the terminal edges of boot_tree */ in Update_IC_Ref_Tree() 166 if (strcmp(ref_tree->labels[target->rank],boot_tree->labels[tip->rank])) { in Update_IC_Ref_Tree() 180 for (j=0; j < 2*boot_tree->notu-2; j++){ in Update_IC_Ref_Tree() 195 for (j=0; j < 2*boot_tree->notu-2; j++) { /* for all the terminal edges of boot_tree */ in Update_IC_Ref_Tree() 209 for (j=0; j < 2*boot_tree->notu-2; j++) { /* for all the terminal edges of boot_tree */ in Update_IC_Ref_Tree() 224 for (j=0; j < 2*boot_tree->notu-2; j++) { /* for all the terminal edges of boot_tree */ in Update_IC_Ref_Tree() 237 void Update_All_IC_Ref_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree, in Update_All_IC_Ref_Tree() argument 249 void Update_IC_Boot_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree, TBE_Node* orig, TBE_Node* target, in Update_IC_Boot_Tree() argument 276 … Update_IC_Boot_Tree(ref_tree, boot_tree, target, target->v1, &(boot_branches[next_boot_edge_id]), in Update_IC_Boot_Tree() 322 void Update_All_IC_Boot_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree, in Update_All_IC_Boot_Tree() argument [all …]
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H A D | tbe.h | 37 void Update_All_IC_Ref_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree, 41 …Tree(TBE_Tree *ref_tree, TBE_Node * orig, TBE_Node* target, TBE_Branch *my_br, TBE_Tree *boot_tree, 45 void Update_IC_Boot_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree, TBE_Node* orig, TBE_Node* target, 51 void Update_All_IC_Boot_Tree(TBE_Tree* ref_tree, TBE_Tree* boot_tree,
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/dports/biology/iqtree/IQ-TREE-2.0.6/booster/ |
H A D | tree.h | 261 void update_i_c_post_order_ref_tree(Tree* ref_tree, Node* orig, Node* target, Tree* boot_tree, shor… 262 void update_all_i_c_post_order_ref_tree(Tree* ref_tree, Tree* boot_tree, short unsigned** i_matrix,… 264 void update_i_c_post_order_boot_tree(Tree* ref_tree, Tree* boot_tree, Node* orig, Node* target, sho… 265 void update_all_i_c_post_order_boot_tree(Tree* ref_tree, Tree* boot_tree, short unsigned** i_matrix…
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H A D | tree.c | 1761 for (j=0; j < boot_tree->nb_edges; j++) { /* for all the terminal edges of boot_tree */ in update_i_c_post_order_ref_tree() 1762 if(boot_tree->a_edges[j]->right->nneigh != 1) continue; in update_i_c_post_order_ref_tree() 1765 if (strcmp(target->name,boot_tree->a_edges[j]->right->name)) { in update_i_c_post_order_ref_tree() 1778 for (j=0; j < boot_tree->nb_edges; j++) in update_i_c_post_order_ref_tree() 1784 if(boot_tree->a_edges[j]->right->nneigh == 1){ in update_i_c_post_order_ref_tree() 1791 …update_i_c_post_order_ref_tree(ref_tree, target, target->neigh[dir], boot_tree, i_matrix, c_matrix… in update_i_c_post_order_ref_tree() 1793 for (j=0; j < boot_tree->nb_edges; j++) { /* for all the terminal edges of boot_tree */ in update_i_c_post_order_ref_tree() 1794 if(boot_tree->a_edges[j]->right->nneigh != 1) continue; in update_i_c_post_order_ref_tree() 1814 …for(i=0; i<n; i++) update_i_c_post_order_ref_tree(ref_tree, root, root->neigh[i], boot_tree, i_mat… in update_all_i_c_post_order_ref_tree() 1850 update_i_c_post_order_boot_tree(ref_tree, boot_tree, target, target->neigh[dir], in update_i_c_post_order_boot_tree() [all …]
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H A D | test.c | 225 …Tree* boot_tree = complete_parse_nh(boot_tree_string, &taxname_lookup_table); /* sets taxname_look… in test_classical_bootstrap() local 236 for (j = 0; j < boot_tree->nb_edges; j++) { in test_classical_bootstrap() 237 if(boot_tree->a_edges[j]->had_zero_length) continue; in test_classical_bootstrap() 240 boot_tree->a_edges[j]->hashtbl[1], in test_classical_bootstrap() 247 if (j == boot_tree->nb_edges) splits_not_found++; in test_classical_bootstrap() 249 free_tree(boot_tree); in test_classical_bootstrap()
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/dports/biology/iqtree/IQ-TREE-2.0.6/tree/ |
H A D | iqtree.cpp | 2652 IQTree *boot_tree; in refineBootTrees() local 2671 boot_tree->on_refine_btree = true; in refineBootTrees() 2672 boot_tree->save_all_trees = 0; in refineBootTrees() 2679 boot_tree->setParams(params); in refineBootTrees() 2682 if (boot_tree->isSuperTree()) in refineBootTrees() 2695 boot_tree->setParams(params); in refineBootTrees() 2696 boot_tree->setLikelihoodKernel(sse); in refineBootTrees() 2714 boot_tree->initializeAllPartialLh(); in refineBootTrees() 2723 boot_tree->optimizeBranches(2); in refineBootTrees() 2745 boot_tree->save_all_trees = 2; in refineBootTrees() [all …]
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/dports/biology/iqtree/IQ-TREE-2.0.6/obsolete/ |
H A D | guidedbootstrap.cpp | 1094 IQTree boot_tree(boot_aln); in runAvHTest() local 1095 runTreeReconstruction(params, orig_model, boot_tree, model_info); in runAvHTest() 1096 boot_tree.setRootNode(params.root); in runAvHTest() 1098 boot_tree.printTree(ss, WT_SORT_TAXA); in runAvHTest() 1288 IQTree boot_tree(boot_aln); in runBootLhTest() local 1289 runTreeReconstruction(params, orig_model, boot_tree, model_info); in runBootLhTest() 1292 evaluateTrees(params, &boot_tree, info, distinct_ids); in runBootLhTest()
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/dports/biology/iqtree/IQ-TREE-2.0.6/main/ |
H A D | phyloanalysis.cpp | 3148 IQTree *boot_tree; in runStandardBootstrap() local 3162 boot_tree = new PhyloTreeMixlen(bootstrap_alignment, 0); in runStandardBootstrap() 3164 boot_tree = new IQTree(bootstrap_alignment); in runStandardBootstrap() 3176 boot_tree->constraintTree.readConstraint(tree->constraintTree); in runStandardBootstrap() 3180 boot_tree->setCheckpoint(tree->getCheckpoint()); in runStandardBootstrap() 3181 boot_tree->num_precision = tree->num_precision; in runStandardBootstrap() 3183 runTreeReconstruction(params, boot_tree); in runStandardBootstrap() 3186 boot_tree->printTree(ss); in runStandardBootstrap() 3213 reportPhyloAnalysis(params, *boot_tree, *model_info); in runStandardBootstrap() 3215 bootstrap_alignment = boot_tree->aln; in runStandardBootstrap() [all …]
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