API reference# topiary.draw topiary.draw.ancestor_data plot_ancestor_data() topiary.draw.core color_to_css() construct_colormap() construct_sizemap() create_name_dict() ete4_to_toytree() get_round_to() parse_position_string() parse_span_color() topiary.draw.prettytree PrettyTree PrettyTree.as_html() PrettyTree.canvas PrettyTree.default_size PrettyTree.draw_node_labels() PrettyTree.draw_node_legend() PrettyTree.draw_nodes() PrettyTree.draw_scale_bar() PrettyTree.legend_ax PrettyTree.plotted_properties PrettyTree.render() PrettyTree.tT PrettyTree.tree_ax PrettyTree.tree_mark topiary.draw.species species_tree() topiary.draw.tree tree() topiary.generax topiary.generax.reconcile reconcile() topiary.io topiary.io.alignments read_fasta_into() write_fasta() write_phy() topiary.io.dataframe read_dataframe() write_dataframe() topiary.io.paralog_patterns load_paralog_patterns() topiary.io.seed df_from_seed() read_seed() topiary.io.tree load_trees() read_tree() write_trees() topiary.muscle topiary.muscle.muscle align() topiary.ncbi topiary.ncbi.blast topiary.ncbi.blast.local local_blast() topiary.ncbi.blast.make make_blast_db() topiary.ncbi.blast.merge merge_and_annotate() merge_blast_df() topiary.ncbi.blast.ncbi ncbi_blast() topiary.ncbi.blast.read check_for_cpu_limit() read_blast_xml() records_to_df() topiary.ncbi.blast.recip recip_blast() topiary.ncbi.blast.util topiary.ncbi.entrez topiary.ncbi.entrez.download ncbi_ftp_download() topiary.ncbi.entrez.proteome get_proteome() get_proteome_ids() topiary.ncbi.entrez.sequences get_sequences() topiary.ncbi.entrez.taxid get_taxid() topiary.opentree topiary.opentree.ott get_df_ott() topiary.opentree.tree df_to_species_tree() topiary.opentree.util ott_to_mrca() ott_to_resolvable() ott_to_species_tree() sort_df_by_taxa() species_to_ott() tree_to_taxa_order() topiary.pastml topiary.pastml.pastml get_ancestral_gaps() topiary.pipeline topiary.pipeline.alignment_to_ancestors alignment_to_ancestors() topiary.pipeline.bootstrap_reconcile bootstrap_reconcile() topiary.pipeline.seed_to_alignment seed_to_alignment() topiary.quality topiary.quality.alignment score_alignment() topiary.quality.polish polish_alignment() topiary.quality.redundancy find_redundancy_cutoff() remove_redundancy() topiary.quality.shrink shrink_aligners() shrink_dataset() shrink_in_species() shrink_redundant() topiary.quality.taxonomic get_merge_blocks() topiary.raxml topiary.raxml.ancestors generate_ancestors() topiary.raxml.bootstrap generate_bootstraps() topiary.raxml.convergence check_convergence() topiary.raxml.model find_best_model() topiary.raxml.tree generate_ml_tree() topiary.reports topiary.reports.cards topiary.reports.cards.ancestor create_ancestor_card() topiary.reports.cards.asr_tree create_asr_tree_card() topiary.reports.cards.duplications create_duplications_card() topiary.reports.cards.input create_input_card() topiary.reports.cards.model create_model_card() topiary.reports.cards.param create_param_card() topiary.reports.cards.species_tree create_species_tree_card() topiary.reports.elements canvas_to_html() create_card() create_element() create_icon_row() create_info_modal() create_main_html() create_modal() create_output_directory() create_row() df_to_table() sequence_box() topiary.reports.reports pipeline_report() tree_report() topiary.util topiary.util.create_nicknames create_nicknames()
