Contents:
plot_ancestor_data()
color_to_css()
construct_colormap()
construct_sizemap()
create_name_dict()
ete3_to_toytree()
get_round_to()
parse_position_string()
parse_span_color()
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
species_tree()
tree()
reconcile()
read_fasta_into()
write_fasta()
write_phy()
read_dataframe()
write_dataframe()
load_paralog_patterns()
df_from_seed()
read_seed()
load_trees()
read_tree()
write_trees()
align()
local_blast()
make_blast_db()
merge_and_annotate()
merge_blast_df()
ncbi_blast()
check_for_cpu_limit()
read_blast_xml()
records_to_df()
recip_blast()
ncbi_ftp_download()
get_proteome()
get_proteome_ids()
get_sequences()
get_taxid()
get_df_ott()
df_to_species_tree()
ott_to_mrca()
ott_to_resolvable()
ott_to_species_tree()
sort_df_by_taxa()
species_to_ott()
tree_to_taxa_order()
get_ancestral_gaps()
alignment_to_ancestors()
bootstrap_reconcile()
seed_to_alignment()
score_alignment()
polish_alignment()
find_redundancy_cutoff()
remove_redundancy()
shrink_aligners()
shrink_dataset()
shrink_in_species()
shrink_redundant()
get_merge_blocks()
generate_ancestors()
generate_bootstraps()
check_convergence()
find_best_model()
generate_ml_tree()
create_ancestor_card()
create_asr_tree_card()
create_duplications_card()
create_input_card()
create_model_card()
create_param_card()
create_species_tree_card()
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()
pipeline_report()
tree_report()
create_nicknames()