Index

A

align() (in module topiary.muscle.muscle)

alignment_to_ancestors() (in module topiary.pipeline.alignment_to_ancestors) as_html() (topiary.draw.prettytree.PrettyTree method)

B

bootstrap_reconcile() (in module topiary.pipeline.bootstrap_reconcile)

C

canvas (topiary.draw.prettytree.PrettyTree property) canvas_to_html() (in module topiary.reports.elements) check_convergence() (in module topiary.raxml.convergence) check_for_cpu_limit() (in module topiary.ncbi.blast.read) color_to_css() (in module topiary.draw.core) construct_colormap() (in module topiary.draw.core) construct_sizemap() (in module topiary.draw.core) create_ancestor_card() (in module topiary.reports.cards.ancestor) create_asr_tree_card() (in module topiary.reports.cards.asr_tree) create_card() (in module topiary.reports.elements) create_duplications_card() (in module topiary.reports.cards.duplications) create_element() (in module topiary.reports.elements)

create_icon_row() (in module topiary.reports.elements) create_info_modal() (in module topiary.reports.elements) create_input_card() (in module topiary.reports.cards.input) create_main_html() (in module topiary.reports.elements) create_modal() (in module topiary.reports.elements) create_model_card() (in module topiary.reports.cards.model) create_name_dict() (in module topiary.draw.core) create_nicknames() (in module topiary.util.create_nicknames) create_output_directory() (in module topiary.reports.elements) create_param_card() (in module topiary.reports.cards.param) create_row() (in module topiary.reports.elements) create_species_tree_card() (in module topiary.reports.cards.species_tree)

D

dataframe_from_fasta() (in module topiary.cli_scripts.dataframe_from_fasta) default_size (topiary.draw.prettytree.PrettyTree property) df_from_seed() (in module topiary.io.seed) df_to_species_tree() (in module topiary.opentree.tree)

df_to_table() (in module topiary.reports.elements) draw_node_labels() (topiary.draw.prettytree.PrettyTree method) draw_node_legend() (topiary.draw.prettytree.PrettyTree method) draw_nodes() (topiary.draw.prettytree.PrettyTree method) draw_scale_bar() (topiary.draw.prettytree.PrettyTree method)

E

ete4_to_toytree() (in module topiary.draw.core)

F

find_best_model() (in module topiary.raxml.model)

find_redundancy_cutoff() (in module topiary.quality.redundancy)

G

generate_ancestors() (in module topiary.raxml.ancestors) generate_bootstraps() (in module topiary.raxml.bootstrap) generate_ml_tree() (in module topiary.raxml.tree) get_ancestral_gaps() (in module topiary.pastml.pastml) get_df_ott() (in module topiary.opentree.ott)

get_merge_blocks() (in module topiary.quality.taxonomic) get_proteome() (in module topiary.ncbi.entrez.proteome) get_proteome_ids() (in module topiary.ncbi.entrez.proteome) get_round_to() (in module topiary.draw.core) get_sequences() (in module topiary.ncbi.entrez.sequences) get_taxid() (in module topiary.ncbi.entrez.taxid)

L

legend_ax (topiary.draw.prettytree.PrettyTree property) load_paralog_patterns() (in module topiary.io.paralog_patterns)

load_trees() (in module topiary.io.tree) local_blast() (in module topiary.ncbi.blast.local)

M

main() (in module topiary.cli_scripts.alignment_to_ancestors) (in module topiary.cli_scripts.bootstrap_reconcile) (in module topiary.cli_scripts.check_installed) (in module topiary.cli_scripts.create_report) (in module topiary.cli_scripts.dataframe_from_fasta) (in module topiary.cli_scripts.fasta_into_dataframe) (in module topiary.cli_scripts.seed_to_alignment) make_blast_db() (in module topiary.ncbi.blast.make) merge_and_annotate() (in module topiary.ncbi.blast.merge) merge_blast_df() (in module topiary.ncbi.blast.merge) module topiary.cli_scripts topiary.cli_scripts.alignment_to_ancestors topiary.cli_scripts.bootstrap_reconcile topiary.cli_scripts.check_installed topiary.cli_scripts.create_report topiary.cli_scripts.dataframe_from_fasta topiary.cli_scripts.fasta_into_dataframe topiary.cli_scripts.seed_to_alignment topiary.draw topiary.draw.ancestor_data topiary.draw.core topiary.draw.prettytree topiary.draw.species topiary.draw.tree topiary.generax topiary.generax.reconcile topiary.io topiary.io.alignments topiary.io.dataframe topiary.io.paralog_patterns topiary.io.seed topiary.io.tree topiary.muscle topiary.muscle.muscle topiary.ncbi topiary.ncbi.blast topiary.ncbi.blast.local topiary.ncbi.blast.make topiary.ncbi.blast.merge topiary.ncbi.blast.ncbi topiary.ncbi.blast.read topiary.ncbi.blast.recip topiary.ncbi.blast.util topiary.ncbi.entrez topiary.ncbi.entrez.download topiary.ncbi.entrez.proteome topiary.ncbi.entrez.sequences topiary.ncbi.entrez.taxid topiary.opentree topiary.opentree.ott topiary.opentree.tree topiary.opentree.util topiary.pastml topiary.pastml.pastml topiary.pipeline topiary.pipeline.alignment_to_ancestors topiary.pipeline.bootstrap_reconcile topiary.pipeline.seed_to_alignment topiary.quality topiary.quality.alignment topiary.quality.polish topiary.quality.redundancy topiary.quality.shrink topiary.quality.taxonomic topiary.raxml topiary.raxml.ancestors topiary.raxml.bootstrap topiary.raxml.convergence topiary.raxml.model topiary.raxml.tree topiary.reports topiary.reports.cards topiary.reports.cards.ancestor topiary.reports.cards.asr_tree topiary.reports.cards.duplications topiary.reports.cards.input topiary.reports.cards.model topiary.reports.cards.param topiary.reports.cards.species_tree topiary.reports.elements topiary.reports.reports topiary.util topiary.util.create_nicknames

N

ncbi_blast() (in module topiary.ncbi.blast.ncbi)

ncbi_ftp_download() (in module topiary.ncbi.entrez.download)

O

ott_to_mrca() (in module topiary.opentree.util)

ott_to_resolvable() (in module topiary.opentree.util) ott_to_species_tree() (in module topiary.opentree.util)

P

parse_position_string() (in module topiary.draw.core) parse_span_color() (in module topiary.draw.core) pipeline_report() (in module topiary.reports.reports)

plot_ancestor_data() (in module topiary.draw.ancestor_data) plotted_properties (topiary.draw.prettytree.PrettyTree property) polish_alignment() (in module topiary.quality.polish) PrettyTree (class in topiary.draw.prettytree)

R

read_blast_xml() (in module topiary.ncbi.blast.read) read_dataframe() (in module topiary.io.dataframe) read_fasta_into() (in module topiary.io.alignments) read_seed() (in module topiary.io.seed) read_tree() (in module topiary.io.tree)

recip_blast() (in module topiary.ncbi.blast.recip) reconcile() (in module topiary.generax.reconcile) records_to_df() (in module topiary.ncbi.blast.read) remove_redundancy() (in module topiary.quality.redundancy) render() (topiary.draw.prettytree.PrettyTree method)

S

score_alignment() (in module topiary.quality.alignment) seed_to_alignment() (in module topiary.pipeline.seed_to_alignment) sequence_box() (in module topiary.reports.elements) shrink_aligners() (in module topiary.quality.shrink) shrink_dataset() (in module topiary.quality.shrink)

shrink_in_species() (in module topiary.quality.shrink) shrink_redundant() (in module topiary.quality.shrink) sort_df_by_taxa() (in module topiary.opentree.util) species_to_ott() (in module topiary.opentree.util) species_tree() (in module topiary.draw.species)

T

topiary.cli_scripts module topiary.cli_scripts.alignment_to_ancestors module topiary.cli_scripts.bootstrap_reconcile module topiary.cli_scripts.check_installed module topiary.cli_scripts.create_report module topiary.cli_scripts.dataframe_from_fasta module topiary.cli_scripts.fasta_into_dataframe module topiary.cli_scripts.seed_to_alignment module topiary.draw module topiary.draw.ancestor_data module topiary.draw.core module topiary.draw.prettytree module topiary.draw.species module topiary.draw.tree module topiary.generax module topiary.generax.reconcile module topiary.io module topiary.io.alignments module topiary.io.dataframe module topiary.io.paralog_patterns module topiary.io.seed module topiary.io.tree module topiary.muscle module topiary.muscle.muscle module topiary.ncbi module topiary.ncbi.blast module topiary.ncbi.blast.local module topiary.ncbi.blast.make module topiary.ncbi.blast.merge module topiary.ncbi.blast.ncbi module topiary.ncbi.blast.read module topiary.ncbi.blast.recip module topiary.ncbi.blast.util module topiary.ncbi.entrez module topiary.ncbi.entrez.download module topiary.ncbi.entrez.proteome module topiary.ncbi.entrez.sequences module topiary.ncbi.entrez.taxid module

topiary.opentree module topiary.opentree.ott module topiary.opentree.tree module topiary.opentree.util module topiary.pastml module topiary.pastml.pastml module topiary.pipeline module topiary.pipeline.alignment_to_ancestors module topiary.pipeline.bootstrap_reconcile module topiary.pipeline.seed_to_alignment module topiary.quality module topiary.quality.alignment module topiary.quality.polish module topiary.quality.redundancy module topiary.quality.shrink module topiary.quality.taxonomic module topiary.raxml module topiary.raxml.ancestors module topiary.raxml.bootstrap module topiary.raxml.convergence module topiary.raxml.model module topiary.raxml.tree module topiary.reports module topiary.reports.cards module topiary.reports.cards.ancestor module topiary.reports.cards.asr_tree module topiary.reports.cards.duplications module topiary.reports.cards.input module topiary.reports.cards.model module topiary.reports.cards.param module topiary.reports.cards.species_tree module topiary.reports.elements module topiary.reports.reports module topiary.util module topiary.util.create_nicknames module tree() (in module topiary.draw.tree) tree_ax (topiary.draw.prettytree.PrettyTree property) tree_mark (topiary.draw.prettytree.PrettyTree property) tree_report() (in module topiary.reports.reports) tree_to_taxa_order() (in module topiary.opentree.util) tT (topiary.draw.prettytree.PrettyTree property)

W

write_dataframe() (in module topiary.io.dataframe) write_fasta() (in module topiary.io.alignments)

write_phy() (in module topiary.io.alignments) write_trees() (in module topiary.io.tree)