Index

_

__version__ (in module biotaphy)

_get_node_label() (in module biotaphy.analyses.anc_dp)

A

add_all_annotations() (in module biotaphy.common.annotators)

AlignmentIOError annotate_tree_with_label() (in module biotaphy.common.annotators)

B

biotaphy module, [1] biotaphy._version module biotaphy.analyses module, [1] biotaphy.analyses.anc_dp module biotaphy.analyses.phylo_beta_diversity module, [1] biotaphy.analyses.site_statistics module biotaphy.client module, [1] biotaphy.client.ot_service_wrapper module, [1] biotaphy.client.ot_service_wrapper.open_tree module, [1] biotaphy.common module biotaphy.common.annotators module biotaphy.common.data_readers module biotaphy.common.plots module biotaphy.common.sequence module biotaphy.data_wrangling module

biotaphy.data_wrangling.matrix module biotaphy.data_wrangling.matrix.accepted_name_data_wrangler module biotaphy.data_wrangling.occurrence module biotaphy.data_wrangling.occurrence.accepted_name_data_wrangler module biotaphy.data_wrangling.species_list module biotaphy.data_wrangling.species_list.accepted_name_data_wrangler module biotaphy.data_wrangling.tree module biotaphy.data_wrangling.tree.accepted_name_data_wrangler module biotaphy.tools module biotaphy.tools.ancestral_distribution module biotaphy.tools.get_tree module biotaphy.tools.phylo_beta_diversity module BiotaphyAcceptedNameMatrixWrangler (class in biotaphy.data_wrangling.matrix.accepted_name_data_wrangler) BiotaphyAcceptedNameOccurrenceWrangler (class in biotaphy.data_wrangling.occurrence.accepted_name_data_wrangler) BiotaphyAcceptedNameSpeciesListWrangler (class in biotaphy.data_wrangling.species_list.accepted_name_data_wrangler) BiotaphyAcceptedNameTreeWrangler (class in biotaphy.data_wrangling.tree.accepted_name_data_wrangler) build_parser() (in module biotaphy.tools.get_tree)

C

calculate_ancestral_distributions() (in module biotaphy.analyses.anc_dp) calculate_continuous_ancestral_states() (in module biotaphy.analyses.anc_dp) calculate_phylo_beta_diversity_jaccard() (in module biotaphy.analyses.phylo_beta_diversity), [1] calculate_phylo_beta_diversity_sorensen() (in module biotaphy.analyses.phylo_beta_diversity), [1] calculate_tree_site_statistics() (in module biotaphy.analyses.site_statistics) cli() (in module biotaphy.tools.ancestral_distribution) (in module biotaphy.tools.get_tree) (in module biotaphy.tools.phylo_beta_diversity)

core_Beta_calc() (in module biotaphy.analyses.phylo_beta_diversity), [1] core_PD_calc() (in module biotaphy.analyses.phylo_beta_diversity), [1] create_distribution_plots() (in module biotaphy.common.plots) create_sequence_list_from_dict() (in module biotaphy.common.data_readers)

D

DESCRIPTION (in module biotaphy.tools.ancestral_distribution) (in module biotaphy.tools.get_tree) (in module biotaphy.tools.phylo_beta_diversity)

G

get_character_matrix_from_sequences_list() (in module biotaphy.common.data_readers) get_config() (in module biotaphy._version) get_fasta() (biotaphy.common.sequence.Sequence method) get_fastq() (biotaphy.common.sequence.Sequence method) get_keywords() (in module biotaphy._version)

get_tip_lengths() (in module biotaphy.analyses.site_statistics) get_versions() (in module biotaphy._version) git_get_keywords() (in module biotaphy._version) git_pieces_from_vcs() (in module biotaphy._version) git_versions_from_keywords() (in module biotaphy._version)

H

HANDLERS (in module biotaphy._version)

I

ID (biotaphy.client.ot_service_wrapper.open_tree.LABEL_FORMAT attribute), [1]

induced_subtree() (in module biotaphy.client.ot_service_wrapper.open_tree), [1] INDUCED_SUBTREE_BASE_URL (in module biotaphy.client.ot_service_wrapper.open_tree)

L

LABEL_FORMAT (class in biotaphy.client.ot_service_wrapper.open_tree), [1]

load_alignment_from_filename() (in module biotaphy.common.data_readers) LONG_VERSION_PY (in module biotaphy._version)

M

MAX_NAMES_PER_REQUEST (in module biotaphy.client.ot_service_wrapper.open_tree) mean_node_height() (in module biotaphy.analyses.site_statistics) mean_tip_length() (in module biotaphy.analyses.site_statistics) median_node_height() (in module biotaphy.analyses.site_statistics) median_tip_length() (in module biotaphy.analyses.site_statistics) module biotaphy, [1] biotaphy._version biotaphy.analyses, [1] biotaphy.analyses.anc_dp biotaphy.analyses.phylo_beta_diversity, [1] biotaphy.analyses.site_statistics biotaphy.client, [1] biotaphy.client.ot_service_wrapper, [1] biotaphy.client.ot_service_wrapper.open_tree, [1] biotaphy.common biotaphy.common.annotators biotaphy.common.data_readers biotaphy.common.plots biotaphy.common.sequence biotaphy.data_wrangling biotaphy.data_wrangling.matrix biotaphy.data_wrangling.matrix.accepted_name_data_wrangler biotaphy.data_wrangling.occurrence biotaphy.data_wrangling.occurrence.accepted_name_data_wrangler biotaphy.data_wrangling.species_list biotaphy.data_wrangling.species_list.accepted_name_data_wrangler biotaphy.data_wrangling.tree biotaphy.data_wrangling.tree.accepted_name_data_wrangler biotaphy.tools biotaphy.tools.ancestral_distribution biotaphy.tools.get_tree biotaphy.tools.phylo_beta_diversity

N

NAME (biotaphy.client.ot_service_wrapper.open_tree.LABEL_FORMAT attribute), [1] name (biotaphy.data_wrangling.matrix.accepted_name_data_wrangler.BiotaphyAcceptedNameMatrixWrangler attribute) (biotaphy.data_wrangling.occurrence.accepted_name_data_wrangler.BiotaphyAcceptedNameOccurrenceWrangler attribute) (biotaphy.data_wrangling.species_list.accepted_name_data_wrangler.BiotaphyAcceptedNameSpeciesListWrangler attribute) (biotaphy.data_wrangling.tree.accepted_name_data_wrangler.BiotaphyAcceptedNameTreeWrangler attribute)

NAME_AND_ID (biotaphy.client.ot_service_wrapper.open_tree.LABEL_FORMAT attribute), [1] node_height_percentile_25() (in module biotaphy.analyses.site_statistics) node_height_percentile_2_5() (in module biotaphy.analyses.site_statistics) node_height_percentile_75() (in module biotaphy.analyses.site_statistics) node_height_percentile_97_5() (in module biotaphy.analyses.site_statistics) NotThisMethod

O

OTT_TAXON_INFO_URL (in module biotaphy.client.ot_service_wrapper.open_tree)

P

pdnew() (in module biotaphy.analyses.phylo_beta_diversity), [1] pep440_split_post() (in module biotaphy._version)

plus_or_dot() (in module biotaphy._version) PRODUCTION_SERVER (in module biotaphy.client.ot_service_wrapper.open_tree)

R

read_csv_alignment_flo() (in module biotaphy.common.data_readers) read_json_alignment_flo() (in module biotaphy.common.data_readers) read_phylip_alignment_flo() (in module biotaphy.common.data_readers) read_table_alignment_flo() (in module biotaphy.common.data_readers) register_vcs_handler() (in module biotaphy._version) render() (in module biotaphy._version) render_git_describe() (in module biotaphy._version) render_git_describe_long() (in module biotaphy._version)

render_pep440() (in module biotaphy._version) render_pep440_branch() (in module biotaphy._version) render_pep440_old() (in module biotaphy._version) render_pep440_post() (in module biotaphy._version) render_pep440_post_branch() (in module biotaphy._version) render_pep440_pre() (in module biotaphy._version) resolve_names_otol() (in module biotaphy.client.ot_service_wrapper.open_tree), [1] run_command() (in module biotaphy._version)

S

sanitize_name() (in module biotaphy.client.ot_service_wrapper.open_tree), [1] Sequence (class in biotaphy.common.sequence)

set_cont_values() (biotaphy.common.sequence.Sequence method) set_qualarr() (biotaphy.common.sequence.Sequence method) set_qualstr() (biotaphy.common.sequence.Sequence method)

T

tip_length_percentile_25() (in module biotaphy.analyses.site_statistics) tip_length_percentile_2_5() (in module biotaphy.analyses.site_statistics)

tip_length_percentile_75() (in module biotaphy.analyses.site_statistics) tip_length_percentile_97_5() (in module biotaphy.analyses.site_statistics) TOLERANCE (in module biotaphy.analyses.site_statistics)

V

version (biotaphy.data_wrangling.matrix.accepted_name_data_wrangler.BiotaphyAcceptedNameMatrixWrangler attribute) (biotaphy.data_wrangling.occurrence.accepted_name_data_wrangler.BiotaphyAcceptedNameOccurrenceWrangler attribute) (biotaphy.data_wrangling.species_list.accepted_name_data_wrangler.BiotaphyAcceptedNameSpeciesListWrangler attribute) (biotaphy.data_wrangling.tree.accepted_name_data_wrangler.BiotaphyAcceptedNameTreeWrangler attribute)

VersioneerConfig (class in biotaphy._version) versions_from_parentdir() (in module biotaphy._version)