Index

A

add_align_method_option() (in module lingpy.cli) add_alignments() (lingpy.align.sca.Alignments method) add_cognate_identifier_option() (in module lingpy.cli) add_cognate_ids() (lingpy.compare.partial.Partial method) add_edge() (lingpy.tests.algorithm.test_extra.Igraph.Graph method) add_entries() (lingpy.basic.parser.QLCParser method) (lingpy.basic.wordlist.Wordlist method) add_format_option() (in module lingpy.cli) add_method_option() (in module lingpy.cli) add_mode_option() (in module lingpy.cli) add_option() (in module lingpy.cli) add_shared_args() (in module lingpy.cli) add_strings_option() (in module lingpy.cli) add_tree_calc_option() (in module lingpy.cli)

add_vertex() (lingpy.tests.algorithm.test_extra.Igraph.Graph method) affinity_propagation() (in module lingpy.algorithm.extra) align() (lingpy.align.pairwise.Pairwise method) (lingpy.align.sca.Alignments method) align_pairs() (lingpy.compare.lexstat.LexStat method) Alignments (class in lingpy.align.sca) alignments (class in lingpy.cli) alm2html() (in module lingpy.convert.html) analyze() (lingpy.compare.phylogeny.PhyBo method) ancestors() (lingpy.thirdparty.cogent.tree.TreeNode method) append() (lingpy.thirdparty.cogent.tree.TreeNode method) as_string() (in module lingpy.util) asciiArt() (lingpy.thirdparty.cogent.tree.TreeNode method) asjp2tokens() (in module lingpy.sequence.sound_classes)

B

balanced() (lingpy.thirdparty.cogent.tree.PhyloNode method) Basemap() (lingpy.tests.compare.test_phylogeny.Bmp method) BasVoc (class in lingpy.meaning.basvoc) bcubes() (in module lingpy.evaluate.acd) best_threshold() (in module lingpy.algorithm.clustering) bidist1() (in module lingpy.compare.strings) bidist2() (in module lingpy.compare.strings)

bidist3() (in module lingpy.compare.strings) bifurcating() (lingpy.thirdparty.cogent.tree.PhyloNode method) bigrams() (in module lingpy.sequence.sound_classes) bisim1() (in module lingpy.compare.strings) bisim2() (in module lingpy.compare.strings) bisim3() (in module lingpy.compare.strings) Bmp (class in lingpy.tests.compare.test_phylogeny)

C

c_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method) c_scores (lingpy.evaluate.apa.EvalMSA attribute) cached_property (class in lingpy.util) calculate() (lingpy.basic.wordlist.Wordlist method) calculate_data() (in module lingpy.basic.ops) capture() (in module lingpy.tests.test_cli) char_from_charstring() (in module lingpy.compare.lexstat) charstring() (in module lingpy.util) check_swaps() (lingpy.evaluate.apa.EvalMSA method) check_tokens() (in module lingpy.sequence.sound_classes) childGroups() (lingpy.thirdparty.cogent.tree.TreeNode method) class2tokens() (in module lingpy.sequence.sound_classes) clean_taxnames() (in module lingpy.basic.ops) Cluster (class in lingpy.tests.algorithm.test_extra) cluster() (lingpy.compare.lexstat.LexStat method) Cluster.AffinityPropagation (class in lingpy.tests.algorithm.test_extra) cmp() (in module lingpy.thirdparty.cogent.tree) cognate_detection() (lingpy.basic.workflow.Workflow method) colexification_network() (in module lingpy.meaning.colexification) colorRange() (in module lingpy.convert.html) comb() (in module lingpy.thirdparty.cogent.tree) combinations2() (in module lingpy.util) Command (class in lingpy.cli) CommandMeta (class in lingpy.cli) community_infomap() (lingpy.tests.algorithm.test_extra.Igraph.Graph method)

compare() (lingpy.meaning.basvoc.Concepticon method) compare_colexifications() (in module lingpy.meaning.colexification) compare_conceptlists() (in module lingpy.meaning.glosses) compare_concepts() (in module lingpy.meaning.glosses) compareByNames() (lingpy.thirdparty.cogent.tree.TreeNode method) compareByPartitions() (lingpy.thirdparty.cogent.tree.PhyloNode method) compareBySubsets() (lingpy.thirdparty.cogent.tree.TreeNode method) compareName() (lingpy.thirdparty.cogent.tree.TreeNode method) compile_dvt() (in module lingpy.data.derive) compile_model() (in module lingpy.data.derive) components (class in lingpy.tests.algorithm.test_extra) Concepticon (class in lingpy.meaning.basvoc) Config (class in lingpy.config) ConfigTest (class in lingpy.tests.test_config) confirm() (in module lingpy.util) copy() (lingpy.thirdparty.cogent.tree.TreeNode method) copyRecursive() (lingpy.thirdparty.cogent.tree.TreeNode method) copyTopology() (lingpy.thirdparty.cogent.tree.TreeNode method) coverage() (in module lingpy.basic.ops) (lingpy.basic.wordlist.Wordlist method) createEdge() (lingpy.thirdparty.cogent.tree.TreeBuilder method) createTransitionMatrix() (lingpy.basic.tree.Tree method) csv2dict() (in module lingpy.read.csv) csv2list() (in module lingpy.read.csv) csv2multidict() (in module lingpy.read.csv) CustomFilter (class in lingpy.log)

D

dbscan() (in module lingpy.algorithm.extra) (lingpy.tests.algorithm.test_extra.Cluster method) Dc() (in module lingpy.thirdparty.linkcomm.link_clustering) debug() (in module lingpy.log) deepcopy() (lingpy.thirdparty.cogent.tree.TreeNode method) dendrogram() (lingpy.tests.convert.test_plot.Sch method) deprecated() (in module lingpy.log)

descendantArray() (lingpy.thirdparty.cogent.tree.TreeNode method) dice() (in module lingpy.compare.strings) diff() (in module lingpy.evaluate.acd) (lingpy.evaluate.apa.EvalPSA method) distance() (lingpy.thirdparty.cogent.tree.PhyloNode method) dump() (in module lingpy.cache)

E

edgeFromEdge() (lingpy.thirdparty.cogent.tree.TreeBuilder method) edit_dist() (in module lingpy.align.pairwise) error() (in module lingpy.log) Eval (class in lingpy.evaluate.apa) EvalMSA (class in lingpy.evaluate.apa)

EvalPSA (class in lingpy.evaluate.apa) evaluate_colexifications() (in module lingpy.meaning.colexification) evaluate_string() (lingpy.sequence.generate.MCPhon method) export() (lingpy.basic.wordlist.Wordlist method) extend() (lingpy.thirdparty.cogent.tree.TreeNode method)

F

failures (lingpy.tests.data.test_sound_class_models.Tests attribute) file_written() (in module lingpy.log) filter() (lingpy.log.CustomFilter method) find_threshold() (in module lingpy.algorithm.clustering) fit_predict() (lingpy.tests.algorithm.test_extra.Cluster.AffinityPropagation method)

flat_cluster() (in module lingpy.algorithm.clustering) flat_upgma() (in module lingpy.algorithm.clustering) fourgrams() (in module lingpy.sequence.sound_classes) fuzzy() (in module lingpy.algorithm.clustering)

G

generate_gml() (lingpy.tests.compare.test_phylogeny.Nx method) get_ACS() (lingpy.compare.phylogeny.PhyBo method) get_all_ngrams() (in module lingpy.sequence.sound_classes) get_AVSD() (lingpy.compare.phylogeny.PhyBo method) get_confidence() (lingpy.align.sca.Alignments method) get_consensus() (in module lingpy.align.sca) (lingpy.align.sca.Alignments method) get_CVSD() (lingpy.compare.phylogeny.PhyBo method) get_dict() (lingpy.basic.wordlist.Wordlist method) (lingpy.meaning.basvoc.BasVoc method) get_distance() (lingpy.basic.tree.Tree method) get_distances() (lingpy.compare.lexstat.LexStat method) get_edge() (lingpy.compare.phylogeny.PhyBo method) get_entries() (lingpy.basic.parser.QLCParserWithRowsAndCols method) get_etymdict() (lingpy.basic.wordlist.Wordlist method) get_frequencies() (lingpy.compare.lexstat.LexStat method) get_gls() (in module lingpy.compare.phylogeny) get_GLS() (lingpy.compare.phylogeny.PhyBo method) get_IVSD() (lingpy.compare.phylogeny.PhyBo method) get_LCA() (lingpy.thirdparty.cogent.tree.TreeNode method) get_level() (in module lingpy.log) get_list() (lingpy.basic.wordlist.Wordlist method) (lingpy.meaning.basvoc.BasVoc method) get_local_peaks() (lingpy.align.multiple.Multiple method) get_log() (in module lingpy.tests.util) get_logger() (in module lingpy.log) get_MLN() (lingpy.compare.phylogeny.PhyBo method) get_MSN() (lingpy.compare.phylogeny.PhyBo method) get_n_ngrams() (in module lingpy.sequence.sound_classes) get_pairwise_alignments() (lingpy.align.multiple.Multiple method) get_paps() (lingpy.basic.wordlist.Wordlist method) get_parser() (in module lingpy.cli) get_PDC() (lingpy.compare.phylogeny.PhyBo method)

get_peaks() (lingpy.align.multiple.Multiple method) get_pid() (lingpy.align.multiple.Multiple method) get_random_distances() (lingpy.compare.lexstat.LexStat method) get_score() (in module lingpy.basic.ops) get_score_dict() (in module lingpy.compare.lexstat) get_scorer() (lingpy.compare.lexstat.LexStat method) get_stats() (lingpy.compare.phylogeny.PhyBo method) get_string() (lingpy.sequence.generate.MCPhon method) get_sublist() (lingpy.meaning.basvoc.BasVoc method) get_subset() (lingpy.compare.lexstat.LexStat method) get_wordlist() (in module lingpy.basic.wordlist) getConnectingEdges() (lingpy.thirdparty.cogent.tree.TreeNode method) getConnectingNode() (lingpy.thirdparty.cogent.tree.TreeNode method) getDistances() (lingpy.thirdparty.cogent.tree.PhyloNode method) (lingpy.thirdparty.cogent.tree.TreeNode method) getDistanceToRoot() (lingpy.basic.tree.Tree method) getEdgeNames() (lingpy.thirdparty.cogent.tree.TreeNode method) getEdgeVector() (lingpy.thirdparty.cogent.tree.TreeNode method) getMaxTipTipDistance() (lingpy.thirdparty.cogent.tree.TreeNode method) getNewick() (lingpy.thirdparty.cogent.tree.PhyloNode method) (lingpy.thirdparty.cogent.tree.TreeNode method) getNewickRecursive() (lingpy.thirdparty.cogent.tree.TreeNode method) getNodeMatchingName() (lingpy.thirdparty.cogent.tree.TreeNode method) getNodeNames() (lingpy.thirdparty.cogent.tree.TreeNode method) getNodesDict() (lingpy.thirdparty.cogent.tree.TreeNode method) getParamValue() (lingpy.thirdparty.cogent.tree.TreeNode method) getSubTree() (lingpy.thirdparty.cogent.tree.TreeNode method) getTipNames() (lingpy.thirdparty.cogent.tree.TreeNode method) getTransitionMatrix() (lingpy.basic.tree.Tree method) gls2gml() (in module lingpy.convert.graph) Graph (class in lingpy.tests.compare.test_phylogeny) Graph() (lingpy.tests.compare.test_phylogeny.Nx method)

H

help (class in lingpy.cli) (lingpy.cli.Command attribute)

HLC (class in lingpy.thirdparty.linkcomm.link_clustering)

I

ident() (in module lingpy.compare.strings) identity() (in module lingpy.util) Igraph (class in lingpy.tests.algorithm.test_extra) Igraph.Graph (class in lingpy.tests.algorithm.test_extra) igraph2networkx() (in module lingpy.convert.graph) indexInParent() (lingpy.thirdparty.cogent.tree.TreeNode method) info() (in module lingpy.log) infomap_clustering() (in module lingpy.algorithm.extra) initialize_edges() (lingpy.thirdparty.linkcomm.link_clustering.HLC method) insert() (lingpy.thirdparty.cogent.tree.TreeNode method) ipa2cls() (lingpy.align.sca.MSA method)

ipa2tokens() (in module lingpy.sequence.sound_classes) isRoot() (lingpy.thirdparty.cogent.tree.TreeNode method) isroot() (lingpy.thirdparty.cogent.tree.TreeNode method) isTip() (lingpy.thirdparty.cogent.tree.TreeNode method) istip() (lingpy.thirdparty.cogent.tree.TreeNode method) iterate_all_sequences() (lingpy.align.multiple.Multiple method) iterate_clusters() (lingpy.align.multiple.Multiple method) iterate_orphans() (lingpy.align.multiple.Multiple method) iterate_similar_gap_sites() (lingpy.align.multiple.Multiple method) iterNontips() (lingpy.thirdparty.cogent.tree.TreeNode method) iterTips() (lingpy.thirdparty.cogent.tree.TreeNode method)

J

jc_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method) jcd() (in module lingpy.compare.strings) jcdn() (in module lingpy.compare.strings)

join() (in module lingpy.util) jsondump() (in module lingpy.util) jsonload() (in module lingpy.util)

L

lastCommonAncestor() (lingpy.thirdparty.cogent.tree.TreeNode method) lca() (lingpy.thirdparty.cogent.tree.TreeNode method) lcs() (in module lingpy.compare.strings) ldn() (in module lingpy.compare.strings) ldn_swap() (in module lingpy.compare.strings) Length (lingpy.thirdparty.cogent.tree.PhyloNode attribute) levelorder() (lingpy.thirdparty.cogent.tree.TreeNode method) lexstat (class in lingpy.cli) LexStat (class in lingpy.compare.lexstat), [1] lib_align() (lingpy.align.multiple.Multiple method) lines_to_text() (in module lingpy.util) lingpy (module) lingpy.algorithm (module) lingpy.algorithm.clustering (module) lingpy.algorithm.cython (module) lingpy.algorithm.cython.compilePYX (module) lingpy.algorithm.extra (module) lingpy.align (module) lingpy.align.multiple (module) lingpy.align.pairwise (module) lingpy.align.sca (module) lingpy.basic (module) lingpy.basic.ops (module) lingpy.basic.parser (module) lingpy.basic.tree (module) lingpy.basic.wordlist (module) lingpy.basic.workflow (module) lingpy.cache (module) lingpy.cli (module) lingpy.compare (module) lingpy.compare.lexstat (module) lingpy.compare.partial (module) lingpy.compare.phylogeny (module) lingpy.compare.strings (module) lingpy.compat (module) lingpy.config (module) lingpy.convert (module) lingpy.convert.graph (module) lingpy.convert.html (module) lingpy.convert.plot (module) lingpy.convert.strings (module) lingpy.convert.tree (module) lingpy.data (module), [1] lingpy.data.derive (module) lingpy.data.ipa (module) lingpy.data.ipa.sampa (module) lingpy.data.model (module) lingpy.evaluate (module) lingpy.evaluate.acd (module) lingpy.evaluate.alr (module) lingpy.evaluate.apa (module) lingpy.log (module) lingpy.meaning (module) lingpy.meaning.basvoc (module) lingpy.meaning.colexification (module) lingpy.meaning.glosses (module) lingpy.read (module) lingpy.read.csv (module) lingpy.read.phylip (module) lingpy.read.qlc (module) lingpy.read.starling (module) lingpy.sequence (module)

lingpy.sequence.generate (module) lingpy.sequence.sound_classes (module) lingpy.settings (module) lingpy.tests (module) lingpy.tests.algorithm (module) lingpy.tests.algorithm.test_cython (module) lingpy.tests.algorithm.test_extra (module) lingpy.tests.align (module) lingpy.tests.align.test_multiple (module) lingpy.tests.align.test_sca (module) lingpy.tests.basic (module) lingpy.tests.basic.test_ops (module) lingpy.tests.basic.test_parser (module) lingpy.tests.basic.test_tree (module) lingpy.tests.basic.test_workflow (module) lingpy.tests.compare (module) lingpy.tests.compare.test_phylogeny (module) lingpy.tests.compare.test_strings (module) lingpy.tests.convert (module) lingpy.tests.convert.test_graph (module) lingpy.tests.convert.test_html (module) lingpy.tests.convert.test_plot (module) lingpy.tests.convert.test_strings (module) lingpy.tests.convert.test_tree (module) lingpy.tests.data (module) lingpy.tests.data.test_derive (module) lingpy.tests.data.test_sound_class_models (module) lingpy.tests.evaluate (module) lingpy.tests.evaluate.test_acd (module) lingpy.tests.evaluate.test_alr (module) lingpy.tests.evaluate.test_apa (module) lingpy.tests.meaning (module) lingpy.tests.meaning.test_colexification (module) lingpy.tests.meaning.test_glosses (module) lingpy.tests.read (module) lingpy.tests.read.test_phylip (module) lingpy.tests.read.test_qlc (module) lingpy.tests.read.test_starling (module) lingpy.tests.sequence (module) lingpy.tests.sequence.test_generate (module) lingpy.tests.test_cache (module) lingpy.tests.test_cli (module) lingpy.tests.test_config (module) lingpy.tests.test_log (module) lingpy.tests.test_util (module) lingpy.tests.thirdparty (module) lingpy.tests.util (module) lingpy.thirdparty (module) lingpy.thirdparty.cogent (module) lingpy.thirdparty.cogent.newick (module) lingpy.thirdparty.cogent.tree (module) lingpy.thirdparty.linkcomm (module) lingpy.thirdparty.linkcomm.link_clustering (module) lingpy.util (module) lingpy_path() (in module lingpy.util) link_clustering() (in module lingpy.algorithm.clustering) load() (in module lingpy.cache) load_dvt() (in module lingpy.data.model) LoadTree() (in module lingpy.thirdparty.cogent.tree) LogTest (class in lingpy.tests.test_log) lowestCommonAncestor() (lingpy.thirdparty.cogent.tree.TreeNode method)

M

main() (in module lingpy.algorithm.cython.compilePYX) (in module lingpy.cli) makeTreeArray() (lingpy.thirdparty.cogent.tree.TreeNode method) matrix2dst() (in module lingpy.convert.strings) matrix2groups() (in module lingpy.algorithm.clustering) matrix2tree() (in module lingpy.algorithm.clustering) maxTipTipDistance() (lingpy.thirdparty.cogent.tree.TreeNode method) MCBasic (class in lingpy.sequence.generate), [1] mcl() (in module lingpy.algorithm.clustering) MCPhon (class in lingpy.sequence.generate), [1] mean_edit_distance() (in module lingpy.evaluate.alr) med() (in module lingpy.evaluate.alr) merge_comms() (lingpy.thirdparty.linkcomm.link_clustering.HLC method) missing_module() (in module lingpy.log)

Model (class in lingpy.data.model), [1] model (lingpy.tests.data.test_sound_class_models.Tests attribute) models (lingpy.tests.data.test_sound_class_models.Tests attribute) MSA (class in lingpy.align.sca) msa2html() (in module lingpy.convert.html) msa2str() (in module lingpy.convert.strings) msa2tex() (in module lingpy.convert.html) mult_align() (in module lingpy.align.multiple) multicombinations2() (in module lingpy.util) Multiple (class in lingpy.align.multiple) multiple (class in lingpy.cli) multistate2nex() (in module lingpy.convert.strings)

N

nameUnnamedNodes() (lingpy.thirdparty.cogent.tree.TreeNode method) neighbor() (in module lingpy.algorithm.clustering) networkx2igraph() (in module lingpy.convert.graph) nodes() (lingpy.tests.compare.test_phylogeny.Graph method) nonTipChildren() (lingpy.thirdparty.cogent.tree.TreeNode method) nontips() (lingpy.thirdparty.cogent.tree.TreeNode method)

normalize_alignment() (in module lingpy.read.qlc) npoint_ap() (in module lingpy.evaluate.acd) nw_align() (in module lingpy.align.pairwise) nwk2gml() (in module lingpy.convert.graph) nwk2tree_matrix() (in module lingpy.convert.tree) Nx (class in lingpy.tests.compare.test_phylogeny)

O

ono_parse() (in module lingpy.sequence.sound_classes)

output() (lingpy.align.sca.Alignments method) (lingpy.align.sca.MSA method) (lingpy.align.sca.PSA method) (lingpy.basic.wordlist.Wordlist method) (lingpy.cli.Command method) (lingpy.compare.lexstat.LexStat method)

P

pairs() (in module lingpy.evaluate.acd) Pairwise (class in lingpy.align.pairwise) pairwise (class in lingpy.cli) pairwise_column_scores (lingpy.evaluate.apa.EvalPSA attribute) pap2csv() (in module lingpy.convert.strings) pap2nex() (in module lingpy.convert.strings) Parent (lingpy.thirdparty.cogent.tree.TreeNode attribute) parse_gloss() (in module lingpy.meaning.glosses) parse_string() (in module lingpy.thirdparty.cogent.newick) Partial (class in lingpy.compare.partial), [1] partial_bcubes() (in module lingpy.evaluate.acd) partial_cluster() (lingpy.compare.partial.Partial method) partition_density() (in module lingpy.algorithm.clustering) path() (in module lingpy.cache) pgrams() (in module lingpy.sequence.sound_classes) PhyBo (class in lingpy.compare.phylogeny), [1] PhyloNode (class in lingpy.thirdparty.cogent.tree) pickle() (lingpy.basic.parser.QLCParser method) pid() (in module lingpy.sequence.sound_classes) plot() (lingpy.tests.compare.test_phylogeny.Plt method) (lingpy.tests.convert.test_plot.Plt method) plot_ACS() (lingpy.compare.phylogeny.PhyBo method) plot_concept_evolution() (in module lingpy.convert.plot) (lingpy.compare.phylogeny.PhyBo method) plot_gls() (in module lingpy.convert.plot)

plot_GLS() (lingpy.compare.phylogeny.PhyBo method) plot_heatmap() (in module lingpy.convert.plot) plot_MLN() (lingpy.compare.phylogeny.PhyBo method) plot_MLN_3d() (lingpy.compare.phylogeny.PhyBo method) plot_MSN() (lingpy.compare.phylogeny.PhyBo method) plot_tree() (in module lingpy.convert.plot) plot_two_concepts() (lingpy.compare.phylogeny.PhyBo method) Plt (class in lingpy.tests.compare.test_phylogeny) (class in lingpy.tests.convert.test_plot) pop() (lingpy.thirdparty.cogent.tree.TreeNode method) postorder() (lingpy.thirdparty.cogent.tree.TreeNode method) pre_and_postorder() (lingpy.thirdparty.cogent.tree.TreeNode method) prefix() (in module lingpy.compare.strings) preorder() (lingpy.thirdparty.cogent.tree.TreeNode method) prog_align() (lingpy.align.multiple.Multiple method) ProgressBar (class in lingpy.util) prosodic_string() (in module lingpy.sequence.sound_classes) prosodic_weights() (in module lingpy.sequence.sound_classes) prune() (lingpy.thirdparty.cogent.tree.PhyloNode method) (lingpy.thirdparty.cogent.tree.TreeNode method) PSA (class in lingpy.align.sca) psa2html() (in module lingpy.convert.html) pw_align() (in module lingpy.align.pairwise) pyx2py() (in module lingpy.algorithm.cython.compilePYX)

Q

QLCParser (class in lingpy.basic.parser)

QLCParserWithRowsAndCols (class in lingpy.basic.parser)

R

r_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method) radial_layout() (in module lingpy.convert.graph) random_tree() (in module lingpy.basic.tree) rc() (in module lingpy.settings), [1], [2] read_asjp() (in module lingpy.read.csv) read_config_file() (in module lingpy.util) read_csv_file() (in module lingpy.util) read_dst() (in module lingpy.read.phylip) read_msa() (in module lingpy.read.qlc) read_qlc() (in module lingpy.read.qlc) read_scorer() (in module lingpy.read.phylip) read_text_file() (in module lingpy.util)

reassignNames() (lingpy.thirdparty.cogent.tree.TreeNode method) reduce_alignment() (in module lingpy.read.qlc) reduce_alignments() (lingpy.align.sca.Alignments method) remove() (lingpy.thirdparty.cogent.tree.TreeNode method) removeNode() (lingpy.thirdparty.cogent.tree.TreeNode method) renumber() (in module lingpy.basic.ops) (lingpy.basic.wordlist.Wordlist method) root() (lingpy.thirdparty.cogent.tree.TreeNode method) rootAtMidpoint() (lingpy.thirdparty.cogent.tree.PhyloNode method) rootedAt() (lingpy.thirdparty.cogent.tree.PhyloNode method) rootedWithTip() (lingpy.thirdparty.cogent.tree.PhyloNode method) run_cli() (lingpy.tests.test_cli.Tests method)

S

sameShape() (lingpy.thirdparty.cogent.tree.TreeNode method) sameTopology() (lingpy.thirdparty.cogent.tree.PhyloNode method) sampa2uni() (in module lingpy.sequence.sound_classes) SCA() (in module lingpy.align.sca) scaleBranchLengths() (lingpy.thirdparty.cogent.tree.PhyloNode method) Sch (class in lingpy.tests.convert.test_plot) scorer2str() (in module lingpy.convert.strings) segment (lingpy.tests.data.test_sound_class_models.Tests attribute) segments (lingpy.tests.data.test_sound_class_models.Tests attribute) separation() (lingpy.thirdparty.cogent.tree.TreeNode method) setdefaults() (in module lingpy.util) setMaxTipTipDistance() (lingpy.thirdparty.cogent.tree.TreeNode method) setParamValue() (lingpy.thirdparty.cogent.tree.TreeNode method) settings (class in lingpy.cli) setTipDistances() (lingpy.thirdparty.cogent.tree.PhyloNode method) setUp() (lingpy.tests.algorithm.test_cython.Tests method) (lingpy.tests.algorithm.test_extra.Tests method) (lingpy.tests.align.test_multiple.Tests method) (lingpy.tests.align.test_sca.TestAlignments method) (lingpy.tests.basic.test_ops.TestOps method) (lingpy.tests.basic.test_parser.TestParser method) (lingpy.tests.basic.test_tree.TestTree method) (lingpy.tests.compare.test_phylogeny.TestPhyBo method) (lingpy.tests.compare.test_strings.TestStrings method) (lingpy.tests.convert.test_plot.TestPlot method) (lingpy.tests.convert.test_tree.TestTree method) (lingpy.tests.data.test_derive.TestDerive method) (lingpy.tests.evaluate.test_acd.Tests method) (lingpy.tests.evaluate.test_alr.Tests method) (lingpy.tests.meaning.test_colexification.TestColexifications method) (lingpy.tests.sequence.test_generate.Tests method) (lingpy.tests.test_config.ConfigTest method) (lingpy.tests.util.WithTempDir method) siblings() (lingpy.thirdparty.cogent.tree.TreeNode method) similarities_unweighted() (in module lingpy.thirdparty.linkcomm.link_clustering)

similarities_weighted() (in module lingpy.thirdparty.linkcomm.link_clustering) single_linkage() (lingpy.thirdparty.linkcomm.link_clustering.HLC method) sorted() (lingpy.thirdparty.cogent.tree.TreeNode method) Sp (class in lingpy.tests.compare.test_phylogeny) sp_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method) star2qlc() (in module lingpy.read.starling) stats (lingpy.tests.compare.test_phylogeny.Sp attribute) string2html() (in module lingpy.convert.html) structalign() (in module lingpy.align.pairwise) subgraphs() (lingpy.tests.algorithm.test_extra.components method) subparser() (lingpy.cli.alignments class method) (lingpy.cli.Command class method) (lingpy.cli.help class method) (lingpy.cli.lexstat class method) (lingpy.cli.multiple class method) (lingpy.cli.pairwise class method) (lingpy.cli.settings class method) (lingpy.cli.wordlist class method) subset() (lingpy.thirdparty.cogent.tree.TreeNode method) subsets() (lingpy.thirdparty.cogent.tree.TreeNode method) sum_of_pairs() (lingpy.align.multiple.Multiple method) sw_align() (in module lingpy.align.pairwise) swap() (in module lingpy.thirdparty.linkcomm.link_clustering) swap_check() (lingpy.align.multiple.Multiple method) syllabify() (in module lingpy.sequence.sound_classes)

T

tearDown() (lingpy.tests.test_log.LogTest method) (lingpy.tests.util.WithTempDir method) TemporaryPath (class in lingpy.util) Test (class in lingpy.tests.test_util) test___get__() (lingpy.tests.align.test_multiple.Tests method) test__calign() (lingpy.tests.algorithm.test_cython.Tests method) test__get_colexifications() (lingpy.tests.meaning.test_colexification.TestColexifications method) test__get_colexifications_by_taxa() (lingpy.tests.meaning.test_colexification.TestColexifications method) test__get_statistics() (lingpy.tests.meaning.test_colexification.TestColexifications method) test__make_graph() (lingpy.tests.meaning.test_colexification.TestColexifications method) test__make_matrix() (lingpy.tests.meaning.test_colexification.TestColexifications method) test__malign() (lingpy.tests.algorithm.test_cython.Tests method) test__nwk_format() (lingpy.tests.convert.test_tree.TestTree method) test__talign() (lingpy.tests.algorithm.test_cython.Tests method) test_add_entries() (lingpy.tests.basic.test_parser.TestParser method) test_affinity_propagation() (lingpy.tests.algorithm.test_extra.Tests method) test_align() (lingpy.tests.align.test_sca.TestAlignments method) test_alignments() (lingpy.tests.test_cli.Tests method) test_alm2html() (lingpy.tests.convert.test_html.Tests method) test_as_string() (in module lingpy.tests.test_util) test_bcubes() (lingpy.tests.evaluate.test_acd.Tests method) test_bidist1() (lingpy.tests.compare.test_strings.TestStrings method) test_bidist2() (lingpy.tests.compare.test_strings.TestStrings method) test_bidist3() (lingpy.tests.compare.test_strings.TestStrings method) test_bisim1() (lingpy.tests.compare.test_strings.TestStrings method) test_bisim2() (lingpy.tests.compare.test_strings.TestStrings method) test_bisim3() (lingpy.tests.compare.test_strings.TestStrings method) test_cache() (lingpy.tests.basic.test_parser.TestParser method) (lingpy.tests.test_cache.TestCache method) test_calculate_data() (lingpy.tests.basic.test_ops.TestOps method) test_clean_taxnames() (lingpy.tests.basic.test_ops.TestOps method) test_clustering() (lingpy.tests.algorithm.test_extra.Tests method) test_colexification_network() (lingpy.tests.meaning.test_colexification.TestColexifications method) test_color_range() (lingpy.tests.convert.test_html.Tests method) test_combinations2() (lingpy.tests.test_util.TestCombinations method) test_compare_colexifications() (lingpy.tests.meaning.test_colexification.TestColexifications method) test_compare_concepts() (lingpy.tests.meaning.test_glosses.Tests method) test_compile_dvt() (lingpy.tests.data.test_derive.TestDerive method) test_compile_model() (lingpy.tests.data.test_derive.TestDerive method) test_conceptlists() (lingpy.tests.meaning.test_glosses.Tests method) test_convenience() (lingpy.tests.test_log.LogTest method) test_corrdist() (lingpy.tests.algorithm.test_cython.Tests method) test_coverage() (lingpy.tests.basic.test_ops.TestOps method) test_data() (in module lingpy.tests.util) test_dbscan() (lingpy.tests.algorithm.test_extra.Tests method) test_default() (lingpy.tests.test_config.ConfigTest method) test_default_config() (lingpy.tests.test_log.LogTest method) test_dice() (lingpy.tests.compare.test_strings.TestStrings method) test_diff() (lingpy.tests.evaluate.test_acd.Tests method) test_dotjoin() (lingpy.tests.test_util.TestJoin method) test_EvalMSA() (lingpy.tests.evaluate.test_apa.Tests method) test_EvalPSA() (lingpy.tests.evaluate.test_apa.Tests method) test_evaluate_colexifications() (lingpy.tests.meaning.test_colexification.TestColexifications method) test_evaluate_string() (lingpy.tests.sequence.test_generate.Tests method) test_existing_config() (lingpy.tests.test_config.ConfigTest method) test_get_confidence() (lingpy.tests.align.test_sca.TestAlignments method) test_get_consensus() (in module lingpy.tests.align.test_sca) (lingpy.tests.align.test_sca.TestAlignments method) test_get_distance() (lingpy.tests.basic.test_tree.TestTree method) test_get_entries() (lingpy.tests.basic.test_parser.TestParser method) test_get_GLS() (lingpy.tests.compare.test_phylogeny.TestPhyBo method) test_get_LCA() (lingpy.tests.basic.test_tree.TestTree method) test_get_local_peaks() (lingpy.tests.align.test_multiple.Tests method) test_get_pairwise_alignments() (lingpy.tests.align.test_multiple.Tests method) test_get_peaks() (lingpy.tests.align.test_multiple.Tests method) test_get_pid() (lingpy.tests.align.test_multiple.Tests method) test_get_string() (lingpy.tests.sequence.test_generate.Tests method) test_getattr() (lingpy.tests.basic.test_parser.TestParser method) test_getDistanceToRoot() (lingpy.tests.basic.test_tree.TestTree method) test_getitem() (lingpy.tests.basic.test_parser.TestParser method) test_ident() (lingpy.tests.compare.test_strings.TestStrings method) test_igraph2networkx() (in module lingpy.tests.convert.test_graph) test_infomap_clustering() (lingpy.tests.algorithm.test_extra.Tests method) test_init() (lingpy.tests.basic.test_parser.TestParser method) test_ipa2tokens() (lingpy.tests.align.test_sca.TestAlignments method) test_iterate_all_sequences() (lingpy.tests.align.test_multiple.Tests method) test_iterate_clusters() (lingpy.tests.align.test_multiple.Tests method) test_iterate_orphans() (lingpy.tests.align.test_multiple.Tests method) test_iterate_similar_gap_sites() (lingpy.tests.align.test_multiple.Tests method) test_jcd() (lingpy.tests.compare.test_strings.TestStrings method) test_jcdn() (lingpy.tests.compare.test_strings.TestStrings method) test_join() (lingpy.tests.test_util.TestJoin method) test_lcs() (lingpy.tests.compare.test_strings.TestStrings method) test_ldn() (lingpy.tests.compare.test_strings.TestStrings method) test_ldn_swap() (lingpy.tests.compare.test_strings.TestStrings method) test_len() (lingpy.tests.basic.test_parser.TestParser method) test_lexstat() (lingpy.tests.test_cli.Tests method) test_lib_align() (lingpy.tests.align.test_multiple.Tests method) test_matrix2dst() (lingpy.tests.convert.test_strings.Tests method) test_med() (lingpy.tests.evaluate.test_alr.Tests method) test_msa2html() (lingpy.tests.convert.test_html.Tests method) test_msa2str() (lingpy.tests.convert.test_strings.Tests method) test_mult_align() (lingpy.tests.align.test_multiple.Tests method) test_multiple() (lingpy.tests.test_cli.Tests method) test_networkx2igraph() (in module lingpy.tests.convert.test_graph) test_new_config() (lingpy.tests.test_config.ConfigTest method) (lingpy.tests.test_log.LogTest method)

test_normalize_alignment() (in module lingpy.tests.read.test_qlc) test_npoint_ap() (in module lingpy.tests.evaluate.test_acd) test_nwk2tree_matrix() (lingpy.tests.convert.test_tree.TestTree method) test_output() (lingpy.tests.align.test_sca.TestAlignments method) (lingpy.tests.align.test_sca.TestMSA method) (lingpy.tests.align.test_sca.TestPSA method) test_pairs() (lingpy.tests.evaluate.test_acd.Tests method) test_pairwise() (lingpy.tests.test_cli.Tests method) test_pap2csv() (lingpy.tests.convert.test_strings.Tests method) test_pap2nex() (lingpy.tests.convert.test_strings.Tests method) test_parse_gloss() (lingpy.tests.meaning.test_glosses.Tests method) test_partial_bcubes() (lingpy.tests.evaluate.test_acd.Tests method) test_plot() (lingpy.tests.compare.test_phylogeny.TestPhyBo method) test_plots() (lingpy.tests.convert.test_plot.TestPlot method) test_prefix() (lingpy.tests.compare.test_strings.TestStrings method) test_prog_align() (lingpy.tests.align.test_multiple.Tests method) test_psa2html() (lingpy.tests.convert.test_html.Tests method) test_random_tree() (in module lingpy.tests.basic.test_tree) test_read_csv_file() (in module lingpy.tests.test_util) test_read_dst() (in module lingpy.tests.read.test_phylip) test_read_msa() (in module lingpy.tests.read.test_qlc) test_read_qlc() (in module lingpy.tests.read.test_qlc) test_read_scorer() (in module lingpy.tests.read.test_phylip) test_reduce_msa() (in module lingpy.tests.read.test_qlc) test_renumber() (lingpy.tests.basic.test_ops.TestOps method) test_scorer2str() (lingpy.tests.convert.test_strings.Tests method) test_settings() (lingpy.tests.test_cli.Tests method) test_star2qlc() (lingpy.tests.read.test_starling.Tests method) test_strings_and_tokens2html() (lingpy.tests.convert.test_html.Tests method) test_sum_of_pairs() (lingpy.tests.align.test_multiple.Tests method) test_swap_check() (lingpy.tests.align.test_multiple.Tests method) test_TextFile() (lingpy.tests.test_util.Test method) test_tridist1() (lingpy.tests.compare.test_strings.TestStrings method) test_tridist2() (lingpy.tests.compare.test_strings.TestStrings method) test_tridist3() (lingpy.tests.compare.test_strings.TestStrings method) test_trigram() (lingpy.tests.compare.test_strings.TestStrings method) test_trisim1() (lingpy.tests.compare.test_strings.TestStrings method) test_trisim2() (lingpy.tests.compare.test_strings.TestStrings method) test_trisim3() (lingpy.tests.compare.test_strings.TestStrings method) test_tsv2triple() (lingpy.tests.basic.test_ops.TestOps method) test_wl2dict() (lingpy.tests.basic.test_ops.TestOps method) test_wl2dst() (lingpy.tests.basic.test_ops.TestOps method) test_wl2multistate() (lingpy.tests.basic.test_ops.TestOps method) test_wl2qlc() (lingpy.tests.basic.test_ops.TestOps method) test_wordlist() (lingpy.tests.test_cli.Tests method) test_Workflow() (lingpy.tests.basic.test_workflow.TestWorkflow method) test_write_text_file() (lingpy.tests.test_util.Test method) test_xdice() (lingpy.tests.compare.test_strings.TestStrings method) test_xxdice() (lingpy.tests.compare.test_strings.TestStrings method) TestAlignments (class in lingpy.tests.align.test_sca) TestCache (class in lingpy.tests.test_cache) TestColexifications (class in lingpy.tests.meaning.test_colexification) TestCombinations (class in lingpy.tests.test_util) TestDerive (class in lingpy.tests.data.test_derive) TestJoin (class in lingpy.tests.test_util) TestMSA (class in lingpy.tests.align.test_sca) TestOps (class in lingpy.tests.basic.test_ops) TestParser (class in lingpy.tests.basic.test_parser) TestPhyBo (class in lingpy.tests.compare.test_phylogeny) TestPlot (class in lingpy.tests.convert.test_plot) TestPSA (class in lingpy.tests.align.test_sca) Tests (class in lingpy.tests.algorithm.test_cython) (class in lingpy.tests.algorithm.test_extra) (class in lingpy.tests.align.test_multiple) (class in lingpy.tests.convert.test_html) (class in lingpy.tests.convert.test_strings) (class in lingpy.tests.data.test_sound_class_models) (class in lingpy.tests.evaluate.test_acd) (class in lingpy.tests.evaluate.test_alr) (class in lingpy.tests.evaluate.test_apa) (class in lingpy.tests.meaning.test_glosses) (class in lingpy.tests.read.test_starling) (class in lingpy.tests.sequence.test_generate) (class in lingpy.tests.test_cli) TestStrings (class in lingpy.tests.compare.test_strings) TestTree (class in lingpy.tests.basic.test_tree) (class in lingpy.tests.convert.test_tree) TestWorkflow (class in lingpy.tests.basic.test_workflow) TextFile (class in lingpy.util) tipChildren() (lingpy.thirdparty.cogent.tree.TreeNode method) tips() (lingpy.thirdparty.cogent.tree.TreeNode method) tipToTipDistances() (lingpy.thirdparty.cogent.tree.PhyloNode method) tmp_path() (lingpy.tests.util.WithTempDir method) token2class() (in module lingpy.sequence.sound_classes) tokens2class() (in module lingpy.sequence.sound_classes) tokens2html() (in module lingpy.convert.html) tokens2morphemes() (in module lingpy.sequence.sound_classes) totalDescendingBranchLength() (lingpy.thirdparty.cogent.tree.PhyloNode method) traverse() (lingpy.thirdparty.cogent.tree.TreeNode method) traverse_recursive() (lingpy.thirdparty.cogent.tree.TreeNode method) TreBor (in module lingpy.compare.phylogeny) Tree (class in lingpy.basic.tree) TreeBuilder (class in lingpy.thirdparty.cogent.tree) TreeError TreeNode (class in lingpy.thirdparty.cogent.tree) TreeParseError tridist1() (in module lingpy.compare.strings) tridist2() (in module lingpy.compare.strings) tridist3() (in module lingpy.compare.strings) trigram() (in module lingpy.compare.strings) trigrams() (in module lingpy.sequence.sound_classes) triple2tsv() (in module lingpy.basic.ops) trisim1() (in module lingpy.compare.strings) trisim2() (in module lingpy.compare.strings) trisim3() (in module lingpy.compare.strings) tsv2triple() (in module lingpy.basic.ops) turchin() (in module lingpy.align.pairwise)

U

unpickle() (lingpy.basic.parser.QLCParser static method) unrooted() (lingpy.thirdparty.cogent.tree.PhyloNode method) unrootedDeepcopy() (lingpy.thirdparty.cogent.tree.PhyloNode method)

update() (lingpy.util.ProgressBar method) upgma() (in module lingpy.algorithm.clustering)

V

values (lingpy.tests.data.test_sound_class_models.Tests attribute)

W

walk() (lingpy.sequence.generate.MCBasic method) warn() (in module lingpy.log) we_align() (in module lingpy.align.pairwise) WithTempDir (class in lingpy.tests.util) wl2dict() (in module lingpy.basic.ops) wl2dst() (in module lingpy.basic.ops) wl2multistate() (in module lingpy.basic.ops)

wl2qlc() (in module lingpy.basic.ops) Wordlist (class in lingpy.basic.wordlist) wordlist (class in lingpy.cli) Workflow (class in lingpy.basic.workflow) write_text_file() (in module lingpy.util) writeToFile() (lingpy.thirdparty.cogent.tree.TreeNode method)

X

xdice() (in module lingpy.compare.strings)

xxdice() (in module lingpy.compare.strings)