Index

A

a (lingpy.basictypes.aligned property) 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_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_sequences() (lingpy.sequence.ngrams.NgramModel method) add_shared_args() (in module lingpy.cli) add_strings_option() (in module lingpy.cli) add_tree_calc_option() (in module lingpy.cli)

affinity_propagation() (in module lingpy.algorithm.extra) align() (lingpy.align.multiple.Multiple method) (lingpy.align.pairwise.Pairwise method) (lingpy.align.sca.Alignments method) align_pairs() (lingpy.compare.lexstat.LexStat method) aligned (class in lingpy.basictypes) 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) average_coverage() (in module lingpy.compare.sanity)

B

balanced() (lingpy.thirdparty.cogent.tree.PhyloNode method) 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.ngrams) bisim1() (in module lingpy.compare.strings) bisim2() (in module lingpy.compare.strings) bisim3() (in module lingpy.compare.strings) BounceAsID (class in lingpy.basic.wordlist)

C

c_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method) c_scores (lingpy.evaluate.apa.EvalMSA attribute) calculate() (lingpy.basic.wordlist.Wordlist method) calculate_data() (in module lingpy.basic.ops) certaintydegree_dist() (in module lingpy.sequence.smoothing) change() (lingpy.basictypes.lists method) char_from_charstring() (in module lingpy.compare.lexstat) charstring() (in module lingpy.util) check_cognates() (in module lingpy.compare.sanity) check_length() (in module lingpy.compare.sanity) check_sequence_length() (in module lingpy.compare.sanity) check_strict_cognates() (in module lingpy.compare.sanity) check_swaps() (lingpy.evaluate.apa.EvalMSA method) check_taxon_names() (in module lingpy.algorithm.clustering) check_tokens() (in module lingpy.sequence.sound_classes) childGroups() (lingpy.thirdparty.cogent.tree.TreeNode method) class2tokens() (in module lingpy.sequence.sound_classes) clean_string() (in module lingpy.sequence.sound_classes) clean_taxnames() (in module lingpy.basic.ops) cluster() (lingpy.compare.lexstat.LexStat method) cmp() (in module lingpy.thirdparty.cogent.tree) codepoint() (in module lingpy.sequence.sound_classes) 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) compare_colexifications() (in module lingpy.meaning.colexification) 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) Config (class in lingpy.config) context_profile() (in module lingpy.sequence.profile) 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) csv2dict() (in module lingpy.read.csv) csv2list() (in module lingpy.read.csv) csv2multidict() (in module lingpy.read.csv) CustomFilter (class in lingpy.log)

D

data_path() (in module lingpy.util) dbscan() (in module lingpy.algorithm.extra) Dc() (in module lingpy.thirdparty.linkcomm.link_clustering) debug() (in module lingpy.log) deepcopy() (lingpy.thirdparty.cogent.tree.TreeNode 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) dotjoin() (in module lingpy.util) dump() (in module lingpy.cache)

E

edgeFromEdge() (lingpy.thirdparty.cogent.tree.TreeBuilder method) edit_dist() (in module lingpy.align.pairwise) ele_dist() (in module lingpy.sequence.smoothing) entropy() (lingpy.sequence.ngrams.NgramModel method) 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.basictypes.lists method) (lingpy.thirdparty.cogent.tree.TreeNode method) extreme_cognates() (in module lingpy.evaluate.acd)

F

file_written() (in module lingpy.log) filter() (lingpy.log.CustomFilter method) find_threshold() (in module lingpy.algorithm.clustering) flat_cluster() (in module lingpy.algorithm.clustering)

flat_upgma() (in module lingpy.algorithm.clustering) fourgrams() (in module lingpy.sequence.ngrams) from_cldf() (in module lingpy.basic.wordlist) (lingpy.basic.wordlist.Wordlist class method) fuzzy() (in module lingpy.algorithm.clustering)

G

generate_all_clusters() (in module lingpy.algorithm.cluster_util) generate_random_cluster() (in module lingpy.algorithm.cluster_util) get_ACS() (lingpy.compare.phylogeny.PhyBo method) get_all_ngrams() (in module lingpy.sequence.ngrams) (in module lingpy.sequence.sound_classes) get_all_ngrams_by_order() (in module lingpy.sequence.ngrams) get_all_posngrams() (in module lingpy.sequence.ngrams) 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) get_distance() (lingpy.basic.tree.Tree method) get_distances() (lingpy.basic.wordlist.Wordlist method) (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) get_local_peaks() (lingpy.align.multiple.Multiple method) get_logger() (in module lingpy.log) get_MLN() (lingpy.compare.phylogeny.PhyBo method) get_msa() (lingpy.align.sca.Alignments method) get_MSN() (lingpy.compare.phylogeny.PhyBo method) get_n_ngrams() (in module lingpy.sequence.ngrams) get_pairwise_alignments() (lingpy.align.multiple.Multiple method) get_paps() (lingpy.basic.wordlist.Wordlist method)

get_parser() (in module lingpy.cli) get_partial_scorer() (lingpy.compare.partial.Partial method) get_PDC() (lingpy.compare.phylogeny.PhyBo method) get_peaks() (lingpy.align.multiple.Multiple method) get_pid() (lingpy.align.multiple.Multiple method) get_posngrams() (in module lingpy.sequence.ngrams) 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_skipngrams() (in module lingpy.sequence.ngrams) get_stats() (lingpy.compare.phylogeny.PhyBo method) get_string() (lingpy.sequence.generate.MCPhon method) get_subset() (lingpy.compare.lexstat.LexStat method) get_tree() (lingpy.basic.wordlist.Wordlist 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) gls2gml() (in module lingpy.convert.graph)

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) 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) integer() (in module lingpy.basictypes) 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) iter_cognates() (lingpy.basic.wordlist.Wordlist method) iter_rows() (in module lingpy.basic.ops) (lingpy.basic.wordlist.Wordlist 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)

L

laplace_dist() (in module lingpy.sequence.smoothing) 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 property) 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) lidstone_dist() (in module lingpy.sequence.smoothing) lines_to_text() (in module lingpy.util) lingpy module lingpy.algorithm module lingpy.algorithm.cluster_util module lingpy.algorithm.clustering module lingpy.algorithm.cython 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.basictypes module lingpy.cache module lingpy.cli module lingpy.compare module lingpy.compare.lexstat module lingpy.compare.partial module lingpy.compare.phylogeny module lingpy.compare.sanity module lingpy.compare.strings module lingpy.compare.util module lingpy.config module lingpy.convert module lingpy.convert.cldf 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.colexification 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.ngrams module lingpy.sequence.profile module lingpy.sequence.smoothing module lingpy.sequence.sound_classes module lingpy.settings 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) lists (class in lingpy.basictypes) load() (in module lingpy.cache) load_dvt() (in module lingpy.data.model) LoadTree() (in module lingpy.thirdparty.cogent.tree) Logging (class in lingpy.log) lowestCommonAncestor() (lingpy.thirdparty.cogent.tree.TreeNode method)

M

main() (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) mcl() (in module lingpy.algorithm.clustering) MCPhon (class in lingpy.sequence.generate) 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) mle_dist() (in module lingpy.sequence.smoothing) Model (class in lingpy.data.model), [1] model_entropy() (lingpy.sequence.ngrams.NgramModel method) module lingpy lingpy.algorithm lingpy.algorithm.cluster_util lingpy.algorithm.clustering lingpy.algorithm.cython lingpy.algorithm.extra lingpy.align lingpy.align.multiple lingpy.align.pairwise lingpy.align.sca lingpy.basic lingpy.basic.ops lingpy.basic.parser lingpy.basic.tree lingpy.basic.wordlist lingpy.basictypes lingpy.cache lingpy.cli lingpy.compare lingpy.compare.lexstat lingpy.compare.partial lingpy.compare.phylogeny lingpy.compare.sanity lingpy.compare.strings lingpy.compare.util lingpy.config lingpy.convert lingpy.convert.cldf lingpy.convert.graph lingpy.convert.html lingpy.convert.plot lingpy.convert.strings lingpy.convert.tree lingpy.data, [1] lingpy.data.derive lingpy.data.ipa lingpy.data.ipa.sampa lingpy.data.model lingpy.evaluate lingpy.evaluate.acd lingpy.evaluate.alr lingpy.evaluate.apa lingpy.log lingpy.meaning lingpy.meaning.colexification lingpy.read lingpy.read.csv lingpy.read.phylip lingpy.read.qlc lingpy.read.starling lingpy.sequence lingpy.sequence.generate lingpy.sequence.ngrams lingpy.sequence.profile lingpy.sequence.smoothing lingpy.sequence.sound_classes lingpy.settings lingpy.thirdparty lingpy.thirdparty.cogent lingpy.thirdparty.cogent.newick lingpy.thirdparty.cogent.tree lingpy.thirdparty.linkcomm lingpy.thirdparty.linkcomm.link_clustering lingpy.util

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) mutate_cluster() (in module lingpy.algorithm.cluster_util) mutual_coverage() (in module lingpy.compare.sanity) mutual_coverage_check() (in module lingpy.compare.sanity) mutual_coverage_subset() (in module lingpy.compare.sanity)

N

nameUnnamedNodes() (lingpy.thirdparty.cogent.tree.TreeNode method) neighbor() (in module lingpy.algorithm.clustering) networkx2igraph() (in module lingpy.convert.graph) nexus_slug() (in module lingpy.util) NgramModel (class in lingpy.sequence.ngrams) 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)

O

ono_parse() (in module lingpy.sequence.sound_classes) order_cluster() (in module lingpy.algorithm.cluster_util) 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 property) 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) perplexity() (lingpy.sequence.ngrams.NgramModel method) pgrams() (in module lingpy.sequence.sound_classes) PhyBo (class in lingpy.compare.phylogeny), [1] PhyloNode (class in lingpy.thirdparty.cogent.tree) pid() (in module lingpy.sequence.sound_classes) 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) 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) profile (class in lingpy.cli) prog_align() (lingpy.align.multiple.Multiple method) 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)

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_choices() (in module lingpy.util) random_cognates() (in module lingpy.evaluate.acd) random_dist() (in module lingpy.sequence.smoothing) random_seqs() (lingpy.sequence.ngrams.NgramModel method) random_tree() (in module lingpy.basic.tree) rc() (in module lingpy.settings), [1], [2] read_asjp() (in module lingpy.read.csv) read_conf() (in module lingpy.basic.parser) read_config_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)

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) score() (lingpy.sequence.ngrams.NgramModel method) scorer2str() (in module lingpy.convert.strings) 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) sgt_dist() (in module lingpy.sequence.smoothing) 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) simple_profile() (in module lingpy.sequence.profile) single_linkage() (lingpy.thirdparty.linkcomm.link_clustering.HLC method) smooth_dist() (in module lingpy.sequence.smoothing) sorted() (lingpy.thirdparty.cogent.tree.TreeNode method) sp_score() (lingpy.evaluate.apa.EvalMSA method) (lingpy.evaluate.apa.EvalPSA method)

star2qlc() (in module lingpy.read.starling) state_score() (lingpy.sequence.ngrams.NgramModel method) string2html() (in module lingpy.convert.html) structalign() (in module lingpy.align.pairwise) 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.profile 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) synonymy() (in module lingpy.compare.sanity)

T

tabjoin() (in module lingpy.util) TemporaryPath (class in lingpy.util) 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) to_cldf() (in module lingpy.convert.cldf) 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) train() (lingpy.sequence.ngrams.NgramModel 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.ngrams) 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

uniform_dist() (in module lingpy.sequence.smoothing) unrooted() (lingpy.thirdparty.cogent.tree.PhyloNode method)

unrootedDeepcopy() (lingpy.thirdparty.cogent.tree.PhyloNode method) upgma() (in module lingpy.algorithm.clustering)

V

valid_cluster() (in module lingpy.algorithm.cluster_util)

W

walk() (lingpy.sequence.generate.MCBasic method) warning() (in module lingpy.log) we_align() (in module lingpy.align.pairwise) wittenbell_dist() (in module lingpy.sequence.smoothing) 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) write_nexus() (in module lingpy.convert.strings) 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)