Index

A

ac2gi() (in module ivy.genbank), [1] add() (ivy.vis.treevis.MultiTreeFigure method), [1] add_ancestor_noderecon() (in module ivy.vis.layers), [1] add_ancrecon() (in module ivy.vis.layers), [1] add_ancrecon_hrm() (in module ivy.vis.layers), [1] add_branchstates() (in module ivy.vis.layers), [1] add_cbar() (in module ivy.vis.layers), [1] add_child() (ivy.chars.cy_tree.cy_tree.Node method) (ivy.tree.Node method), [1] add_circles() (in module ivy.vis.layers), [1] add_circles_branches() (in module ivy.vis.layers), [1] add_highlight() (in module ivy.vis.layers), [1] add_hrm_hiddenstate_recon() (in module ivy.vis.layers), [1] add_image() (in module ivy.vis.layers), [1] add_label() (in module ivy.vis.layers), [1] add_label_chars() (in module ivy.chars.cy_tree.newick) (in module ivy.newick), [1] add_layer() (ivy.vis.treevis.TreeFigure method), [1] add_legend() (in module ivy.vis.layers), [1] add_mkmr_heatmap() (in module ivy.vis.layers), [1] add_node_heatmap() (in module ivy.vis.layers), [1] add_overview_rect() (ivy.vis.treevis.OverviewTree method), [1] add_phylorate() (in module ivy.vis.layers), [1] add_pie() (in module ivy.vis.layers), [1] add_squares() (in module ivy.vis.layers), [1] add_text() (in module ivy.vis.layers), [1] add_tipstates() (in module ivy.vis.layers), [1]

add_tree_heatmap() (in module ivy.vis.layers), [1] adjust_limits() (in module ivy.vis.axes_utils), [1] adjust_xspine() (ivy.vis.treevis.Tree method), [1] ages2lengths() (in module ivy.ages), [1] AIC() (in module ivy.chars.hrm), [1] Alignment (class in ivy.vis.alignment), [1] AlignmentFigure (class in ivy.vis.alignment), [1] alnfig() (in module ivy.interactive), [1] Alpha() (in module ivy.birthdeath), [1] anc_recon_cat() (in module ivy.chars.recon), [1] anc_recon_mkmr() (in module ivy.chars.recon), [1] ancstates() (in module ivy.chars.catpars), [1] any_equal() (in module ivy.chars.hrm), [1] ape_node_idx() (ivy.tree.Node method), [1] artist_data_extents() (in module ivy.vis.axes_utils), [1] ascii() (ivy.tree.Node method), [1] AsciiBuffer (class in ivy.ascii), [1] autocollapse() (in module ivy.autocollapse), [1] autocollapse_info() (in module ivy.autocollapse), [1] autoheight() (ivy.vis.hardcopy.TreeFigure method), [1] average_nchanges() (in module ivy.chars.recon), [1] axes (ivy.vis.treevis.TreeFigure attribute), [1] axes_enter() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] axes_leave() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1]

B

batch() (in module ivy.genbank), [1] Beta() (in module ivy.birthdeath), [1] bft() (ivy.chars.cy_tree.cy_tree.Node method) bgrep() (ivy.tree.Node method), [1] binary_deltran() (in module ivy.chars.catpars), [1] Bipart (class in ivy.bipart), [1]

bisect_branch() (ivy.tree.Node method), [1] blast() (in module ivy.genbank), [1] blast_closest() (in module ivy.genbank), [1] BokehTree (class in ivy.vis.bokehtree), [1] brownian() (in module ivy.chars.evolve), [1]

C

C() (in module ivy.tree), [1] calc_node_positions() (in module ivy.layout), [1] (in module ivy.layout_polar), [1] cartesian() (in module ivy.layout), [1] cbar() (ivy.vis.treevis.TreeFigure method), [1] center_node() (ivy.vis.treevis.Tree method), [1] center_x() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.treevis.Tree method), [1] center_y() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.treevis.Tree method), [1] children (ivy.chars.cy_tree.cy_tree.Node attribute) circle_selected_nodes() (ivy.vis.treevis.Tree method), [1] clade_dimensions() (ivy.vis.treevis.Tree method), [1] clade_height_pixels() (ivy.vis.treevis.Tree method), [1] clade_sizes() (in module ivy.tree), [1] clades() (ivy.tree.Node method), [1] cladesizes1() (in module ivy.chars.cy_tree.cy_tree) cladesizes2() (in module ivy.chars.cy_tree.cy_tree) cladesizes3() (in module ivy.chars.cy_tree.cy_tree) cladesizes4() (in module ivy.chars.cy_tree.cy_tree) clear() (ivy.ordereddict.OrderedDict method), [1] (ivy.vis.treevis.MultiTreeFigure method), [1] cls() (in module ivy.tree), [1] cluster_models() (in module ivy.chars.hrm), [1] collapse() (ivy.tree.Node method), [1] color_blender_1() (in module ivy.vis.layers), [1] color_map() (in module ivy.vis.layers), [1] colorbar_legend() (in module ivy.vis.layers), [1] compare() (in module ivy.bipart), [1]

compare_trees() (in module ivy.bipart), [1] competence() (ivy.chars.mk_mr.ModelOrderMetropolis method), [1] (ivy.chars.mk_mr.SwitchpointMetropolis method), [1] compute() (ivy.bipart.Bipart method), [1] condKendall1948() (in module ivy.birthdeath), [1] condPrN() (in module ivy.birthdeath), [1] conflict() (in module ivy.bipart), [1] connect_events() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure method), [1] connectors() (ivy.vis.bokehtree.BokehTree method), [1] convert() (in module ivy.storage), [1] Coordinates (class in ivy.layout), [1] (class in ivy.layout_polar), [1] copy() (in module ivy.pyperclip), [1] (ivy.ordereddict.OrderedDict method), [1] (ivy.storage.Counter method), [1] (ivy.tree.Node method), [1] Counter (class in ivy.storage), [1] create_ancrecon_ars() (in module ivy.chars.recon), [1] create_branch_artists() (ivy.vis.treevis.Tree method), [1] create_fastas() (in module ivy.genbank), [1] create_hrm_ar() (in module ivy.chars.hrm), [1] create_likelihood_function_hrm_mk_MLE() (in module ivy.chars.hrm), [1] create_likelihood_function_mk() (in module ivy.chars.mk), [1] create_likelihood_function_multimk() (in module ivy.chars.mk_mr), [1] create_likelihood_function_multimk_mods() (in module ivy.chars.mk_mr), [1] create_mk_ar() (in module ivy.chars.mk), [1] create_mk_model() (in module ivy.chars.bayesian_models), [1] create_mkmr_ar() (in module ivy.chars.mk_mr), [1] create_mkmr_mb_ar() (in module ivy.chars.mk_mr), [1] create_multi_mk_model() (in module ivy.chars.bayesian_models), [1]

D

default_costmatrix() (in module ivy.chars.catpars), [1] Demo (class in ivy.demo), [1] demo() (in module ivy.demo), [1] depth_length_preorder_traversal() (in module ivy.layout), [1] (in module ivy.layout_polar), [1] descendants() (ivy.tree.Node method), [1] detail (ivy.vis.hardcopy.TreeFigure attribute), [1]

downpass() (in module ivy.chars.catpars), [1] draw_labels() (ivy.vis.treevis.Tree method), [1] drawlabels() (ivy.vis.bokehtree.BokehTree method), [1] drawtree() (ivy.vis.bokehtree.BokehTree method), [1] drop_tip() (ivy.tree.Node method), [1]

E

elements() (ivy.storage.Counter method), [1] excise() (ivy.tree.Node method), [1] extract_gbac() (in module ivy.genbank), [1] extract_gene() (in module ivy.genbank), [1]

extract_Qparams() (in module ivy.chars.hrm), [1] extract_regimes() (in module ivy.chars.hrm), [1] extract_selected() (ivy.vis.alignment.Alignment method), [1]

F

fetch_aclist() (in module ivy.genbank), [1] fetch_DNA_seqs() (in module ivy.genbank), [1] fetch_gilist() (in module ivy.genbank), [1] fetch_study() (in module ivy.treebase), [1] fetchaln() (in module ivy.chars.cy_tree.nexus) (in module ivy.nexus), [1] fetchseq() (in module ivy.genbank), [1] fetchtax() (in module ivy.genbank), [1] fill_distinct_regime_Q() (in module ivy.chars.hrm), [1] fill_model_mk() (in module ivy.chars.hrm_bayesian), [1] fill_model_mr_Q() (in module ivy.chars.mk_mr), [1] fill_model_Q() (in module ivy.chars.hrm), [1] (in module ivy.chars.hrm_bayesian), [1] fill_Q_layout() (in module ivy.chars.hrm), [1] fill_Q_matrix() (in module ivy.chars.hrm), [1] find() (in module ivy.align), [1] (ivy.tree.Node method), [1] (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] find_id() (in module ivy.align), [1] find_stop_codons() (in module ivy.sequtil), [1] findall() (ivy.tree.Node method), [1]

finditer() (in module ivy.sequtil), [1] fit_hrm() (in module ivy.chars.hrm), [1] fit_hrm_distinct_regimes() (in module ivy.chars.hrm), [1] fit_hrm_mkARD() (in module ivy.chars.hrm), [1] fit_hrm_mkSimple() (in module ivy.chars.hrm), [1] fit_hrm_model() (in module ivy.chars.hrm), [1] fit_hrm_model_likelihood() (in module ivy.chars.hrm), [1] fit_hrm_qidx() (in module ivy.chars.hrm), [1] fit_hrm_randstartingpoints() (in module ivy.chars.hrm), [1] fit_Mk() (in module ivy.chars.mk), [1] fit_mk_bayes() (in module ivy.chars.bayesian_models), [1] fitMkARD() (in module ivy.chars.mk), [1] fitMkER() (in module ivy.chars.mk), [1] fitMkSym() (in module ivy.chars.mk), [1] format_mod() (in module ivy.chars.hrm), [1] fromkeys() (ivy.ordereddict.OrderedDict class method), [1] (ivy.storage.Counter class method), [1]

G

gapcols() (in module ivy.align), [1] gapidx() (in module ivy.sequtil), [1] get() (ivy.data.Matrix method), [1] (ivy.tree.Node method), [1] get_childstates() (in module ivy.chars.recon), [1] get_indices() (in module ivy.chars.bayesian_models), [1] get_root() (ivy.tree.Node method), [1] get_siblings() (ivy.tree.Node method), [1] get_visible_nodes() (ivy.vis.treevis.Tree method), [1] getcb() (in module ivy.pyperclip), [1]

getplot() (ivy.vis.treevis.MultiTreeFigure method), [1] gi2tax() (in module ivy.genbank), [1] gi2webenv() (in module ivy.genbank), [1] global_step() (ivy.chars.mk_mr.SwitchpointMetropolis method), [1] gradient_segment_horz() (in module ivy.vis.layers), [1] graft() (ivy.tree.Node method), [1] grep() (ivy.tree.Node method), [1] gtkGetClipboard() (in module ivy.pyperclip), [1] gtkSetClipboard() (in module ivy.pyperclip), [1]

H

hardcopy() (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] highlight() (ivy.vis.bokehtree.BokehTree method), [1] (ivy.vis.treevis.TreeFigure method), [1] highlight_find() (ivy.vis.alignment.Alignment method), [1] home() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.hardcopy.TreeFigure method), [1] (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.OverviewTree method), [1] (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1]

hrm_allmodels_bayes() (in module ivy.chars.hrm_bayesian), [1] hrm_bayesian() (in module ivy.chars.bayesian_models), [1] hrm_disctinct_regimes_likelihoodfunc() (in module ivy.chars.hrm), [1] hrm_mk() (in module ivy.chars.hrm), [1]

I

index() (ivy.chars.cy_tree.cy_tree.Tree method) index_array() (ivy.data.Rows method), [1] inds_from_switchpoint_cython() (in module ivy.chars.mk_mr), [1] initialize_subplots() (ivy.vis.alignment.AlignmentFigure method), [1] (ivy.vis.treevis.TreeFigure method), [1] internals() (ivy.tree.Node method), [1] is_monotypic() (in module ivy.chars.discrete), [1] is_same_tree() (ivy.tree.Node method), [1] is_valid_model() (in module ivy.chars.hrm_bayesian), [1] iscompatible() (ivy.bipart.Bipart method), [1] isleaf (ivy.chars.cy_tree.cy_tree.Node attribute) ismono() (ivy.tree.Node method), [1] isroot (ivy.chars.cy_tree.cy_tree.Node attribute) items() (ivy.ordereddict.OrderedDict method), [1] iter_bboxes() (in module ivy.vis.axes_utils), [1] iterchildren() (ivy.chars.cy_tree.cy_tree.Node method) iteritems() (ivy.ordereddict.OrderedDict method), [1] iterkeys() (ivy.ordereddict.OrderedDict method), [1] iterleaves() (ivy.tree.Node method), [1] iternodes() (ivy.chars.cy_tree.cy_tree.Node method) (ivy.tree.Node method), [1] iternodes_cached() (ivy.tree.Node method), [1] itervalues() (ivy.ordereddict.OrderedDict method), [1] ivy (module) ivy.ages (module), [1] ivy.align (module), [1] ivy.ascii (module), [1] ivy.autocollapse (module), [1] ivy.bipart (module), [1] ivy.birthdeath (module), [1] ivy.chars (module) ivy.chars.bayesian_models (module), [1] ivy.chars.catpars (module), [1] ivy.chars.cy_tree (module) ivy.chars.cy_tree.cy_tree (module) ivy.chars.cy_tree.newick (module) ivy.chars.cy_tree.nexus (module) ivy.chars.cy_tree.test (module) ivy.chars.discrete (module), [1] ivy.chars.evolve (module), [1] ivy.chars.expokit (module) ivy.chars.expokit.cyexpokit (module), [1]

ivy.chars.expokit.setup (module), [1] ivy.chars.hrm (module), [1] ivy.chars.hrm_bayesian (module), [1] ivy.chars.mk (module), [1] ivy.chars.mk_mr (module), [1] ivy.chars.recon (module), [1] ivy.chars.sse (module) ivy.chars.sse.sse (module) ivy.contrasts (module), [1] ivy.data (module), [1] ivy.demo (module), [1] ivy.examples (module) ivy.genbank (module), [1] ivy.interactive (module), [1] ivy.layout (module), [1] ivy.layout_polar (module), [1] ivy.ltt (module), [1] ivy.matrix (module), [1] ivy.newick (module), [1] ivy.nexus (module), [1] ivy.ordereddict (module), [1] ivy.pyperclip (module), [1] ivy.r_funcs (module), [1] ivy.sequtil (module), [1] ivy.sim (module) ivy.sim.discrete_sim (module), [1] ivy.storage (module), [1] ivy.tree (module), [1] ivy.treebase (module), [1] ivy.vis (module) ivy.vis.alignment (module), [1] ivy.vis.axes_utils (module), [1] ivy.vis.bokehtree (module), [1] ivy.vis.colors (module), [1] ivy.vis.events (module), [1] ivy.vis.hardcopy (module), [1] ivy.vis.layers (module), [1] ivy.vis.tree (module) ivy.vis.treevis (module), [1]

K

keep_tip() (ivy.tree.Node method), [1] Kendall1948() (in module ivy.birthdeath), [1]

keys() (ivy.ordereddict.OrderedDict method), [1]

L

label (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute) labeled() (ivy.tree.Node method), [1] ladderize() (ivy.tree.Node method), [1] (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.TreeFigure method), [1] layout() (ivy.vis.bokehtree.BokehTree method), [1] (ivy.vis.treevis.RadialTree method), [1] (ivy.vis.treevis.Tree method), [1] leaf_distances() (ivy.tree.Node method), [1] leaf_pixelsep() (ivy.vis.treevis.Tree method), [1] leafsets() (ivy.tree.Node method), [1] leaves (ivy.chars.cy_tree.cy_tree.Node attribute) leaves() (ivy.tree.Node method), [1] left (ivy.chars.cy_tree.cy_tree.Node attribute) leftchild (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute)

leftsib (ivy.chars.cy_tree.cy_tree.Node attribute) length (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute) lf_mk_mr_midbranch() (in module ivy.chars.mk_mr), [1] lf_mk_mr_midbranch_mods() (in module ivy.chars.mk_mr), [1] lgrep() (ivy.tree.Node method), [1] load_chars() (in module ivy.tree), [1] local_step() (ivy.chars.mk_mr.SwitchpointMetropolis method), [1] locs_from_switchpoint() (in module ivy.chars.mk_mr), [1] logLT() (in module ivy.birthdeath), [1] ltt() (in module ivy.ltt), [1]

M

macGetClipboard() (in module ivy.pyperclip), [1] macSetClipboard() (in module ivy.pyperclip), [1] make_identity_regime() (in module ivy.chars.hrm), [1] make_modelorder_stoch() (in module ivy.chars.mk_mr), [1] make_qmat_stoch() (in module ivy.chars.hrm_bayesian), [1] make_qmat_stoch_mk() (in module ivy.chars.hrm_bayesian), [1] make_regime_type_combos() (in module ivy.chars.hrm), [1] make_switchpoint_stoch() (in module ivy.chars.mk_mr), [1] makehovertool() (ivy.vis.bokehtree.BokehTree method), [1] makeroot() (ivy.tree.Node method), [1] mark_named() (ivy.vis.treevis.Tree method), [1] Matrix (class in ivy.data), [1] max_tippath() (ivy.tree.Node method), [1] MaxDict (class in ivy.storage), [1] merge_fastas() (in module ivy.genbank), [1]

min_ages() (in module ivy.ages), [1] minstates() (in module ivy.chars.catpars), [1] mk() (in module ivy.chars.mk), [1] mk_allmodels_bayes() (in module ivy.chars.hrm_bayesian), [1] mk_mr_midbranch() (in module ivy.chars.mk_mr), [1] mk_multi_bayes() (in module ivy.chars.mk_mr), [1] mk_results() (in module ivy.chars.bayesian_models), [1] ModelOrderMetropolis (class in ivy.chars.mk_mr), [1] monotypic_clade_size() (in module ivy.chars.discrete), [1] most_common() (ivy.storage.Counter method), [1] mrca() (ivy.tree.Node method), [1] MultiTreeFigure (class in ivy.vis.treevis), [1] muscle() (in module ivy.align), [1] musclep() (in module ivy.align), [1]

N

Nbar() (in module ivy.birthdeath), [1] nchildren (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute) new_hrm_model() (in module ivy.chars.hrm_bayesian), [1] Newick (class in ivy.chars.cy_tree.nexus) (class in ivy.nexus), [1] nexus_iter() (in module ivy.chars.cy_tree.newick) (in module ivy.newick), [1] ni (ivy.chars.cy_tree.cy_tree.Node attribute) nleaves (ivy.chars.cy_tree.cy_tree.Tree attribute) nnodes (ivy.chars.cy_tree.cy_tree.Tree attribute)

Node (class in ivy.chars.cy_tree.cy_tree) (class in ivy.tree), [1] nodeLikelihood() (in module ivy.chars.discrete), [1] nodepos() (in module ivy.layout), [1] NoTO() (in module ivy.chars.discrete), [1] nshifts() (in module ivy.chars.bayesian_models), [1] ntaxa() (ivy.tree.Node method), [1] number_connected() (in module ivy.chars.hrm_bayesian), [1]

O

on_nodes_selected() (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.TreeFigure method), [1] onbuttonrelease() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] onclick() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] ondrag() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] onkeypress() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] onpick() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] onscroll() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1]

onselect() (in module ivy.vis.events), [1] (ivy.vis.alignment.AlignmentFigure static method), [1] optimize_regime() (in module ivy.chars.hrm), [1] order_subtrees_by_size() (ivy.tree.Node method), [1] OrderedDict (class in ivy.ordereddict), [1] organism_id() (in module ivy.genbank), [1] OverviewTree (class in ivy.vis.treevis), [1]

P

p2y() (ivy.vis.treevis.Tree method), [1] pairwise_merge() (in module ivy.chars.hrm), [1] parent (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute) parse() (in module ivy.chars.cy_tree.newick) (in module ivy.newick), [1] (ivy.chars.cy_tree.nexus.Newick method) (ivy.nexus.Newick method), [1] parse_ampersand_comment() (in module ivy.chars.cy_tree.newick) (in module ivy.newick), [1] parse_chars() (in module ivy.treebase), [1] parse_charsets() (in module ivy.treebase), [1] parse_embedded_comment() (ivy.chars.cy_tree.newick.Tokenizer method) (ivy.newick.Tokenizer method), [1] parse_nexml() (in module ivy.treebase), [1] parse_otus() (in module ivy.treebase), [1] parse_states() (in module ivy.treebase), [1] parse_trees() (in module ivy.treebase), [1] parse_treesblock() (in module ivy.chars.cy_tree.nexus) (in module ivy.nexus), [1] parsimony_recon() (in module ivy.chars.recon), [1] paste() (in module ivy.pyperclip), [1] phylorate() (in module ivy.r_funcs), [1]

PIC() (in module ivy.contrasts), [1] picked() (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] plot_aln() (ivy.vis.alignment.Alignment method), [1] plot_tree() (ivy.vis.treevis.Tree method), [1] point() (ivy.layout.Coordinates method), [1] pop() (ivy.ordereddict.OrderedDict method), [1] popitem() (ivy.ordereddict.OrderedDict method), [1] populate() (ivy.chars.cy_tree.nexus.Newick method) (ivy.nexus.Newick method), [1] postiter() (ivy.chars.cy_tree.cy_tree.Node method) (ivy.tree.Node method), [1] postorder (ivy.chars.cy_tree.cy_tree.Tree attribute) preiter() (ivy.tree.Node method), [1] prN() (in module ivy.birthdeath), [1] propose() (ivy.chars.hrm_bayesian.QmatMetropolis method), [1] (ivy.chars.hrm_bayesian.QmatMetropolis_mk method), [1] (ivy.chars.mk_mr.ModelOrderMetropolis method), [1] (ivy.chars.mk_mr.SwitchpointMetropolis method), [1] prune() (ivy.chars.cy_tree.cy_tree.Node method) (ivy.tree.Node method), [1] pscore() (in module ivy.chars.recon), [1] putstr() (ivy.ascii.AsciiBuffer method), [1]

Q

QmatMetropolis (class in ivy.chars.hrm_bayesian), [1] QmatMetropolis_mk (class in ivy.chars.hrm_bayesian), [1] qsd() (in module ivy.chars.mk), [1]

qtGetClipboard() (in module ivy.pyperclip), [1] qtSetClipboard() (in module ivy.pyperclip), [1]

R

r_hat_crown() (in module ivy.birthdeath), [1] r_hat_stem() (in module ivy.birthdeath), [1] RadialTree (class in ivy.vis.treevis), [1] random() (in module ivy.demo), [1] random_tree_location() (in module ivy.chars.mk_mr), [1] read() (in module ivy.align), [1] (in module ivy.tree), [1] readaln() (in module ivy.interactive), [1] readEL() (in module ivy.matrix), [1] readmany() (in module ivy.tree), [1] readtree() (in module ivy.interactive), [1] rectselect() (ivy.vis.treevis.OverviewTree method), [1] (ivy.vis.treevis.Tree method), [1] redraw() (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.OverviewTree method), [1] (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] redraw_keeptemp() (ivy.vis.treevis.OverviewTree method), [1] reindex() (ivy.tree.Node method), [1] reject() (ivy.chars.hrm_bayesian.QmatMetropolis method), [1] (ivy.chars.hrm_bayesian.QmatMetropolis_mk method), [1] (ivy.chars.mk_mr.ModelOrderMetropolis method), [1] (ivy.chars.mk_mr.SwitchpointMetropolis method), [1] remove_child() (ivy.tree.Node method), [1]

remove_layer() (ivy.vis.treevis.TreeFigure method), [1] remove_redundant_regimes() (in module ivy.chars.hrm), [1] remove_singletons() (in module ivy.tree), [1] render() (in module ivy.ascii), [1] render_multipage() (ivy.vis.hardcopy.TreeFigure method), [1] reorder_layers() (ivy.vis.treevis.TreeFigure method), [1] reroot() (ivy.tree.Node method), [1] right (ivy.chars.cy_tree.cy_tree.Node attribute) rightsib (ivy.chars.cy_tree.cy_tree.Node attribute) (ivy.chars.cy_tree.cy_tree.Tree attribute) root (ivy.chars.cy_tree.cy_tree.Tree attribute) rootpath() (ivy.tree.Node method), [1] rootpath_length() (ivy.tree.Node method), [1] rootpathlen() (ivy.chars.cy_tree.cy_tree.Tree method) round_step_size() (in module ivy.chars.mk_mr), [1] Rows (class in ivy.data), [1]

S

savefig() (ivy.vis.hardcopy.TreeFigure method), [1] scale_cpos() (in module ivy.ascii), [1] scroll() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.treevis.Tree method), [1] search_taxonomy() (in module ivy.genbank), [1] select_nodes() (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] select_rectangle() (ivy.vis.alignment.Alignment method), [1] selected (ivy.vis.alignment.AlignmentFigure attribute), [1] (ivy.vis.treevis.TreeFigure attribute), [1] seqrec_taxid() (in module ivy.genbank), [1] set_iternode_cache() (ivy.tree.Node method), [1] set_name() (ivy.vis.treevis.Tree method), [1] set_positions() (ivy.vis.treevis.TreeFigure method), [1] set_relative_width() (ivy.vis.hardcopy.TreeFigure method), [1] set_root() (ivy.vis.bokehtree.BokehTree method), [1] (ivy.vis.treevis.Tree method), [1] set_rpos() (in module ivy.ascii), [1] set_scaled() (ivy.vis.treevis.Tree method), [1] set_target() (ivy.vis.treevis.OverviewTree method), [1] setcb() (in module ivy.pyperclip), [1]

setdefault() (ivy.ordereddict.OrderedDict method), [1] ShiftedGamma() (in module ivy.chars.hrm_bayesian), [1] show() (ivy.demo.Demo method), [1] (ivy.vis.alignment.AlignmentFigure method), [1] (ivy.vis.treevis.MultiTreeFigure method), [1] (ivy.vis.treevis.TreeFigure method), [1] sim_discrete() (in module ivy.sim.discrete_sim), [1] smooth() (in module ivy.ages), [1] smooth_cpos() (in module ivy.ascii), [1] smooth_xpos() (in module ivy.layout), [1] (in module ivy.layout_polar), [1] split_blocks() (in module ivy.chars.cy_tree.nexus) (in module ivy.nexus), [1] sse_get_lambda() (in module ivy.chars.discrete), [1] sse_get_mu() (in module ivy.chars.discrete), [1] sse_get_qij() (in module ivy.chars.discrete), [1] start_codons() (in module ivy.genbank), [1] Storage (class in ivy.storage), [1] subtree_mapping() (ivy.tree.Node method), [1] sum_to_root() (in module ivy.ascii), [1] SwitchpointMetropolis (class in ivy.chars.mk_mr), [1]

T

tango() (in module ivy.vis.colors), [1] test() (in module ivy.layout_polar), [1] (in module ivy.ltt), [1] test_brownian() (in module ivy.chars.evolve), [1] test_parse_comment() (in module ivy.chars.cy_tree.newick) (in module ivy.newick), [1] tip_age_rank_sum() (in module ivy.chars.discrete), [1] tiplabels() (ivy.tree.Node method), [1] tipstates() (ivy.vis.treevis.TreeFigure method), [1] toggle_branchlabels() (ivy.vis.treevis.TreeFigure method), [1] toggle_layer() (ivy.vis.treevis.TreeFigure method), [1] toggle_leaflabels() (ivy.vis.treevis.TreeFigure method), [1] toggle_overview() (ivy.vis.treevis.TreeFigure method), [1] Tokenizer (class in ivy.chars.cy_tree.newick) (class in ivy.newick), [1]

traverse() (in module ivy.ltt), [1] (in module ivy.tree), [1] Tree (class in ivy.chars.cy_tree.cy_tree) (class in ivy.vis.treevis), [1] tree_from_ivy() (in module ivy.chars.cy_tree.cy_tree) tree_map() (in module ivy.chars.mk_mr), [1] treefig() (in module ivy.interactive), [1] TreeFigure (class in ivy.vis.hardcopy), [1] (class in ivy.vis.treevis), [1] treename (ivy.chars.cy_tree.cy_tree.Node attribute) TreeSet (class in ivy.bipart), [1] trimpos() (in module ivy.genbank), [1] twoS_colormaker() (in module ivy.vis.layers), [1] twoS_twoR_colormaker() (in module ivy.vis.layers), [1]

U

unique_models() (in module ivy.chars.hrm_bayesian), [1] update() (ivy.ordereddict.OrderedDict method), [1] (ivy.storage.Counter method), [1]

UpdatingRect (class in ivy.vis.alignment), [1] (class in ivy.vis.events), [1] (class in ivy.vis.treevis), [1] uppass() (in module ivy.chars.catpars), [1]

V

valid_indices() (in module ivy.chars.bayesian_models), [1] values() (ivy.ordereddict.OrderedDict method), [1]

vcv() (in module ivy.matrix), [1]

W

window2data() (ivy.vis.treevis.Tree method), [1] winGetClipboard() (in module ivy.pyperclip), [1] winSetClipboard() (in module ivy.pyperclip), [1]

write() (in module ivy.align), [1] (in module ivy.tree), [1] (ivy.tree.Node method), [1] write_newick() (in module ivy.tree), [1]

X

xclipGetClipboard() (in module ivy.pyperclip), [1] xclipSetClipboard() (in module ivy.pyperclip), [1] xoffset() (ivy.vis.treevis.Tree method), [1]

xselGetClipboard() (in module ivy.pyperclip), [1] xselSetClipboard() (in module ivy.pyperclip), [1] xy() (in module ivy.vis.layers), [1]

Y

ypp() (ivy.vis.treevis.Tree method), [1]

Z

zoom() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.alignment.AlignmentFigure method), [1] (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] zoom_clade() (ivy.vis.treevis.Tree method), [1] (ivy.vis.treevis.TreeFigure method), [1] zoom_cxy() (ivy.vis.alignment.Alignment method), [1] (ivy.vis.treevis.Tree method), [1]

zoom_nodes() (ivy.vis.treevis.Tree method), [1] zx() (ivy.vis.treevis.TreeFigure method), [1] zy() (ivy.vis.treevis.TreeFigure method), [1]