topiary
latest
Contents:
Installation
Protocol
Pipeline details
Determining taxonomic scope
Drawing Trees
Data structures and API philosophy
API reference
topiary
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
W
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
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
ete3_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
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.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.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)
Read the Docs
v: latest
Versions
latest
stable
main
Downloads
On Read the Docs
Project Home
Builds