diff --git a/reference/reference_tree.html b/reference/reference_tree.html index 157a31acb..4d9d87d50 100644 --- a/reference/reference_tree.html +++ b/reference/reference_tree.html @@ -750,23 +750,22 @@

Tree
-populate(size, names_library=None, reuse_names=False, random_branches=False, branch_range=(0, 1), support_range=(0, 1))
+populate(size, names_library=None, random_branches=False, dist_range=(0, 1), support_range=(0, 1))

Populate current node with branches generating a random topology.

+

All the nodes added will either be leaves or have two branches.

Parameters:
    -

  • names_library (None) – If provided, names library (list, -set, dict, etc.) will be used to name nodes.

    • -

  • reuse_names (False) – If True, node names will not be -necessarily unique, which makes the process a bit more -efficient.

    • -

  • random_branches (False) – If True, branch distances and -support values will be randomized.

    • -

  • branch_range ((0,1)) – If random_branches is True, this -range of values will be used to generate random distances.

    • -

  • support_range ((0,1)) – If random_branches is True, this -range of values will be used to generate random branch -support values.

    • +

  • size – Number of leaves to add. The necessary +intermediate nodes will be created too.

    • +

  • names_library – Collection (list or set) used to name leaves. +If None, leaves will be named using short letter sequences.

    • +

  • random_branches – If True, branch distances and support +values will be randomized.

    • +

  • dist_range – Range (tuple with min and max) of distances +used to generate branch distances if random_branches is True.

    • +

  • support_range – Range (tuple with min and max) of distances +used to generate branch supports if random_branches is True.

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"welcome-to-ete-s-documentation"]], "Contents:": [[2, null]], "Indices and tables": [[2, "indices-and-tables"]], "Reference Guide": [[3, "reference-guide"]], "Clustering": [[4, "module-ete4.clustering.clustertree"]], "NCBITaxa": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "PhyloTree class": [[6, "phylotree-class"]], "SeqGroup": [[7, "module-ete4.coretype.seqgroup"]], "Tree": [[8, "tree"]], "Treeview": [[9, "treeview"]], "TreeStyle": [[9, "treestyle"]], "NodeStyle": [[9, "nodestyle"]], "Faces": [[9, "faces"]], "ETE Tutorial": [[10, "ete-tutorial"]], "Phylogenetic trees": [[11, "phylogenetic-trees"]], "Overview": [[11, "overview"]], "Linking phylogenetic trees with multiple sequence alignments": [[11, "linking-phylogenetic-trees-with-multiple-sequence-alignments"]], "Visualization of phylogenetic trees": [[11, "visualization-of-phylogenetic-trees"]], "Adding taxonomic information": [[11, "adding-taxonomic-information"]], "Automatic control of species info": [[11, "automatic-control-of-species-info"]], "Automatic (custom) control of the species info": [[11, "automatic-custom-control-of-the-species-info"]], "Manual control of the species info": [[11, "manual-control-of-the-species-info"]], "Working with the Tree structure": [[12, "working-with-the-tree-structure"]], "Trees": [[12, "trees"]], "Reading and writing newick trees": [[12, "reading-and-writing-newick-trees"]], "Creating a tree": [[12, "creating-a-tree"]], "Reading newick trees": [[12, "reading-newick-trees"]], "Writing newick trees": [[12, "writing-newick-trees"]], "Understanding ETE trees": [[12, "understanding-ete-trees"]], "Basic tree attributes": [[12, "basic-tree-attributes"]], "The meaning of the \u201croot node\u201d in unrooted trees": [[12, "the-meaning-of-the-root-node-in-unrooted-trees"]], "Browsing trees (traversing)": [[12, "browsing-trees-traversing"]], "Getting leaves, descendants and node\u2019s relatives": [[12, "getting-leaves-descendants-and-node-s-relatives"]], "Traversing (browsing) trees": [[12, "traversing-browsing-trees"]], "Advanced traversing": [[12, "advanced-traversing"]], "Collapsing nodes while traversing": [[12, "collapsing-nodes-while-traversing"]], "Iterators or lists?": [[12, "iterators-or-lists"]], "Finding nodes by their properties": [[12, "finding-nodes-by-their-properties"]], "Search_all nodes matching a given criteria": [[12, "search-all-nodes-matching-a-given-criteria"]], "Search nodes matching a given criteria (iteration)": [[12, "search-nodes-matching-a-given-criteria-iteration"]], "Find the first common ancestor": [[12, "find-the-first-common-ancestor"]], "Custom searching functions": [[12, "custom-searching-functions"]], "Shortcuts": [[12, "shortcuts"]], "Checking the monophyly of properties within a tree": [[12, "checking-the-monophyly-of-properties-within-a-tree"]], "Caching tree content for faster lookup operations": [[12, "caching-tree-content-for-faster-lookup-operations"]], "Node annotation": [[12, "node-annotation"]], "Comparing trees": [[12, "comparing-trees"]], "Distances between trees": [[12, "distances-between-trees"]], "Robinson-Foulds distance": [[12, "robinson-foulds-distance"]], "Modifying tree topology": [[12, "modifying-tree-topology"]], "Creating trees from scratch": [[12, "creating-trees-from-scratch"]], "How to delete/eliminate or remove/detach nodes": [[12, "how-to-delete-eliminate-or-remove-detach-nodes"]], "Pruning trees": [[12, "pruning-trees"]], "Concatenating trees": [[12, "concatenating-trees"]], "Copying (duplicating) trees": [[12, "copying-duplicating-trees"]], "Solving multifurcations": [[12, "solving-multifurcations"]], "Tree rooting": [[12, "tree-rooting"]], "Working with branch distances": [[12, "working-with-branch-distances"]], "Getting distances between nodes": [[12, "getting-distances-between-nodes"]], "Getting midpoint outgroup": [[12, "getting-midpoint-outgroup"]]}, "indexentries": {"clustertree (class in ete4.clustering.clustertree)": [[4, "ete4.clustering.clustertree.ClusterTree"]], "__init__() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.__init__"]], "deviation (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.deviation"]], "ete4.clustering.clustertree": [[4, "module-ete4.clustering.clustertree"]], "get_dunn() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_dunn"]], "get_silhouette() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.get_silhouette"]], "intercluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intercluster_dist"]], "intracluster_dist (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.intracluster_dist"]], "leaf_profiles() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.leaf_profiles"]], "link_to_arraytable() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.link_to_arraytable"]], "module": [[4, "module-ete4.clustering.clustertree"], [5, "module-ete4.ncbi_taxonomy.ncbiquery"], [7, "module-ete4.coretype.seqgroup"]], "profile (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.profile"]], "set_distance_function() (clustertree method)": [[4, "ete4.clustering.clustertree.ClusterTree.set_distance_function"]], "silhouette (clustertree property)": [[4, "ete4.clustering.clustertree.ClusterTree.silhouette"]], "ncbitaxa (class in ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa"]], "__init__() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.__init__"]], "annotate_tree() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.annotate_tree"]], "ete4.ncbi_taxonomy.ncbiquery": [[5, "module-ete4.ncbi_taxonomy.ncbiquery"]], "get_broken_branches() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_broken_branches"]], "get_common_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_common_names"]], "get_descendant_taxa() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_descendant_taxa"]], "get_fuzzy_name_translation() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_fuzzy_name_translation"]], "get_lineage() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage"]], "get_lineage_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_lineage_translator"]], "get_name_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_name_translator"]], "get_rank() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_rank"]], "get_taxid_translator() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_taxid_translator"]], "get_topology() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.get_topology"]], "is_taxadb_up_to_date() (in module ete4.ncbi_taxonomy.ncbiquery)": [[5, "ete4.ncbi_taxonomy.ncbiquery.is_taxadb_up_to_date"]], "translate_to_names() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.translate_to_names"]], "update_taxonomy_database() (ncbitaxa method)": [[5, "ete4.ncbi_taxonomy.ncbiquery.NCBITaxa.update_taxonomy_database"]], "evolevent (class in ete4.phylo)": [[6, "ete4.phylo.EvolEvent"]], "phylotree (class in ete4)": [[6, "ete4.PhyloTree"]], "annotate_gtdb_taxa() (phylotree method)": [[6, "ete4.PhyloTree.annotate_gtdb_taxa"]], "annotate_ncbi_taxa() (phylotree method)": [[6, "ete4.PhyloTree.annotate_ncbi_taxa"]], "collapse_lineage_specific_expansions() (phylotree method)": [[6, "ete4.PhyloTree.collapse_lineage_specific_expansions"]], "get_age() (phylotree method)": [[6, "ete4.PhyloTree.get_age"]], "get_age_balanced_outgroup() (phylotree method)": [[6, "ete4.PhyloTree.get_age_balanced_outgroup"]], "get_descendant_evol_events() (phylotree method)": [[6, "ete4.PhyloTree.get_descendant_evol_events"]], "get_farthest_oldest_leaf() (phylotree method)": [[6, "ete4.PhyloTree.get_farthest_oldest_leaf"]], "get_farthest_oldest_node() (phylotree method)": [[6, "ete4.PhyloTree.get_farthest_oldest_node"]], "get_my_evol_events() (phylotree method)": [[6, "ete4.PhyloTree.get_my_evol_events"]], "get_speciation_trees() (phylotree method)": [[6, "ete4.PhyloTree.get_speciation_trees"]], "get_species() (phylotree method)": [[6, "ete4.PhyloTree.get_species"]], "iter_species() (phylotree method)": [[6, "ete4.PhyloTree.iter_species"]], "link_to_alignment() (phylotree method)": [[6, "ete4.PhyloTree.link_to_alignment"]], "ncbi_compare() (phylotree method)": [[6, "ete4.PhyloTree.ncbi_compare"]], "reconcile() (phylotree method)": [[6, "ete4.PhyloTree.reconcile"]], "set_species_naming_function() (phylotree method)": [[6, "ete4.PhyloTree.set_species_naming_function"]], "species (phylotree property)": [[6, "ete4.PhyloTree.species"]], "split_by_dups() (phylotree method)": [[6, "ete4.PhyloTree.split_by_dups"]], "write() (phylotree method)": [[6, "ete4.PhyloTree.write"]], "seqgroup (class in ete4.coretype.seqgroup)": [[7, "ete4.coretype.seqgroup.SeqGroup"]], "__init__() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.__init__"]], "ete4.coretype.seqgroup": [[7, "module-ete4.coretype.seqgroup"]], "get_entries() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.get_entries"]], "get_seq() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.get_seq"]], "iter_entries() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.iter_entries"]], "set_seq() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.set_seq"]], "write() (seqgroup method)": [[7, "ete4.coretype.seqgroup.SeqGroup.write"]], "tree (class in ete4)": [[8, "ete4.Tree"]], "__init__() (tree method)": [[8, "ete4.Tree.__init__"]], "add_child() (tree method)": [[8, "ete4.Tree.add_child"]], "add_children() (tree method)": [[8, "ete4.Tree.add_children"]], "add_face() (tree method)": [[8, "ete4.Tree.add_face"]], "add_face_smartview() (tree method)": [[8, "ete4.Tree.add_face_smartview"]], "add_face_treeview() (tree method)": [[8, "ete4.Tree.add_face_treeview"]], "add_feature() (tree method)": [[8, "ete4.Tree.add_feature"]], "add_features() (tree method)": [[8, "ete4.Tree.add_features"]], "add_prop() (tree method)": [[8, "ete4.Tree.add_prop"]], "add_props() (tree method)": [[8, "ete4.Tree.add_props"]], "add_sister() (tree method)": [[8, "ete4.Tree.add_sister"]], "ancestors() (tree method)": [[8, "ete4.Tree.ancestors"]], "check_monophyly() (tree method)": [[8, "ete4.Tree.check_monophyly"]], "children (tree attribute)": [[8, "ete4.Tree.children"]], "collapsed_faces (tree attribute)": [[8, "ete4.Tree.collapsed_faces"]], "common_ancestor() (tree method)": [[8, "ete4.Tree.common_ancestor"]], "compare() (tree method)": [[8, "ete4.Tree.compare"]], "cophenetic_matrix() (tree method)": [[8, "ete4.Tree.cophenetic_matrix"]], "copy() (tree method)": [[8, "ete4.Tree.copy"]], "del_feature() (tree method)": [[8, "ete4.Tree.del_feature"]], "del_prop() (tree method)": [[8, "ete4.Tree.del_prop"]], "delete() (tree method)": [[8, "ete4.Tree.delete"]], "descendants() (tree method)": [[8, "ete4.Tree.descendants"]], "describe() (tree method)": [[8, "ete4.Tree.describe"]], "detach() (tree method)": [[8, "ete4.Tree.detach"]], "dist (tree attribute)": [[8, "ete4.Tree.dist"]], "edges() (tree method)": [[8, "ete4.Tree.edges"]], "expand_polytomies() (tree method)": [[8, "ete4.Tree.expand_polytomies"]], "explore() (tree method)": [[8, "ete4.Tree.explore"]], "faces (tree attribute)": [[8, "ete4.Tree.faces"]], "from_parent_child_table() (tree static method)": [[8, "ete4.Tree.from_parent_child_table"]], "from_skbio() (tree static method)": [[8, "ete4.Tree.from_skbio"]], "get_cached_content() (tree method)": [[8, "ete4.Tree.get_cached_content"]], "get_children() (tree method)": [[8, "ete4.Tree.get_children"]], "get_closest_leaf() (tree method)": [[8, "ete4.Tree.get_closest_leaf"]], "get_distance() (tree method)": [[8, "ete4.Tree.get_distance"]], "get_farthest_leaf() (tree method)": [[8, "ete4.Tree.get_farthest_leaf"]], "get_farthest_node() (tree method)": [[8, "ete4.Tree.get_farthest_node"]], "get_midpoint_outgroup() (tree method)": [[8, "ete4.Tree.get_midpoint_outgroup"]], "get_monophyletic() (tree method)": [[8, "ete4.Tree.get_monophyletic"]], "get_sisters() (tree method)": [[8, "ete4.Tree.get_sisters"]], "get_topology_id() (tree method)": [[8, "ete4.Tree.get_topology_id"]], "id (tree attribute)": [[8, "ete4.Tree.id"]], "img_style (tree property)": [[8, "ete4.Tree.img_style"]], "init_from_ete() (tree method)": [[8, "ete4.Tree.init_from_ete"]], "init_from_newick() (tree method)": [[8, "ete4.Tree.init_from_newick"]], "is_collapsed (tree property)": [[8, "ete4.Tree.is_collapsed"]], "is_initialized (tree property)": [[8, "ete4.Tree.is_initialized"]], "is_leaf (tree attribute)": [[8, "ete4.Tree.is_leaf"]], "is_monophyletic() (tree method)": [[8, "ete4.Tree.is_monophyletic"]], "is_root (tree attribute)": [[8, "ete4.Tree.is_root"]], "iter_prepostorder() (tree method)": [[8, "ete4.Tree.iter_prepostorder"]], "ladderize() (tree method)": [[8, "ete4.Tree.ladderize"]], "leaf_names() (tree method)": [[8, "ete4.Tree.leaf_names"]], "leaves() (tree method)": [[8, "ete4.Tree.leaves"]], "level (tree attribute)": [[8, "ete4.Tree.level"]], "lineage() (tree method)": [[8, "ete4.Tree.lineage"]], "name (tree attribute)": [[8, "ete4.Tree.name"]], "phonehome() (tree method)": [[8, "ete4.Tree.phonehome"]], "pop_child() (tree method)": [[8, "ete4.Tree.pop_child"]], "populate() (tree method)": [[8, "ete4.Tree.populate"]], "props (tree attribute)": [[8, "ete4.Tree.props"]], "prune() (tree method)": [[8, "ete4.Tree.prune"]], "remove_child() (tree method)": [[8, "ete4.Tree.remove_child"]], "remove_children() (tree method)": [[8, "ete4.Tree.remove_children"]], "remove_sister() (tree method)": [[8, "ete4.Tree.remove_sister"]], "render() (tree method)": [[8, "ete4.Tree.render"]], "resolve_polytomy() (tree method)": [[8, "ete4.Tree.resolve_polytomy"]], "robinson_foulds() (tree method)": [[8, "ete4.Tree.robinson_foulds"]], "root (tree attribute)": [[8, "ete4.Tree.root"]], "search_ancestors() (tree method)": [[8, "ete4.Tree.search_ancestors"]], "search_descendants() (tree method)": [[8, "ete4.Tree.search_descendants"]], "search_leaves_by_name() (tree method)": [[8, "ete4.Tree.search_leaves_by_name"]], "search_nodes() (tree method)": [[8, "ete4.Tree.search_nodes"]], "set_outgroup() (tree method)": [[8, "ete4.Tree.set_outgroup"]], "set_outgroup_v2() (tree method)": [[8, "ete4.Tree.set_outgroup_v2"]], "set_style() (tree method)": [[8, "ete4.Tree.set_style"]], "show() (tree method)": [[8, "ete4.Tree.show"]], "size (tree attribute)": [[8, "ete4.Tree.size"]], "sm_style (tree property)": [[8, "ete4.Tree.sm_style"]], "sort_descendants() (tree method)": [[8, "ete4.Tree.sort_descendants"]], "standardize() (tree method)": [[8, "ete4.Tree.standardize"]], "support (tree 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in ete4)": [[9, "ete4.TreeStyle"]], "build_regions() (seqmotifface method)": [[9, "ete4.SeqMotifFace.build_regions"]], "fits() (face method)": [[9, "ete4.Face.fits"]], "fits() (seqmotifface method)": [[9, "ete4.SeqMotifFace.fits"]], "fits() (textface method)": [[9, "ete4.TextFace.fits"]]}}) \ No newline at end of file