Index

A

AbstractGene (class in pyham.abstractgene) add_child() (pyham.abstractgene.HOG method) add_gene() (pyham.genome.Genome method) add_genome_to_node() (pyham.taxonomy.Taxonomy method) add_hogs_via_GeneExtId() (pyham.ham.ParserFilter method)

add_hogs_via_GeneIntId() (pyham.ham.ParserFilter method) add_hogs_via_hogId() (pyham.ham.ParserFilter method) add_map() (pyham.mapper.MapLateral method) (pyham.mapper.MapResults method) (pyham.mapper.MapVertical method) AncestralGenome (class in pyham.genome)

B

buildFilter() (pyham.ham.ParserFilter method)

C

compare_genomes_lateral() (pyham.ham.Ham method) compare_genomes_vertically() (pyham.ham.Ham method) compute_tree_profile_full() (pyham.TreeProfile.TreeProfile method)

computeTP_hog() (pyham.TreeProfile.TreeProfile method) create_iHam() (pyham.ham.Ham method) create_tree_profile() (pyham.ham.Ham method)

E

export() (pyham.TreeProfile.TreeProfile method)

export_as_html() (pyham.TreeProfile.TreeProfile method) ExtantGenome (class in pyham.genome)

F

find_by_id() (pyham.abstractgene.HOG method)

format() (pyham.validation.ValidationReport method) from_newick() (pyham.taxonomy.Taxonomy class method)

G

Gene (class in pyham.abstractgene) Genome (class in pyham.genome) get_all_descendant_genes() (pyham.abstractgene.HOG method) get_all_descendant_genes_clustered_by_species() (pyham.abstractgene.HOG method) get_all_descendant_hog_levels() (pyham.abstractgene.HOG method) get_all_descendant_hogs() (pyham.abstractgene.HOG method) get_ancestral_clustering() (pyham.genome.AncestralGenome method) get_ancestral_genome_by_mrca_of_genome_set() (pyham.ham.Ham method) get_ancestral_genome_by_name() (pyham.ham.Ham method) get_ancestral_genome_by_taxon() (pyham.ham.Ham method) get_at_level() (pyham.abstractgene.AbstractGene method) get_dict_extant_genes() (pyham.ham.Ham method) get_dict_top_level_hogs() (pyham.ham.Ham method) get_dict_xref() (pyham.abstractgene.Gene method) get_duplicated() (pyham.mapper.MapLateral method) (pyham.mapper.MapResults method) (pyham.mapper.MapVertical method) get_extant_genome_by_name() (pyham.ham.Ham method) get_extant_taxa_by_name() (pyham.taxonomy.Taxonomy method) get_gained() (pyham.mapper.MapLateral method) (pyham.mapper.MapResults method) (pyham.mapper.MapVertical method) get_gene_by_id() (pyham.ham.Ham method) get_genes_by_external_id() (pyham.ham.Ham method) get_genome_from_taxnode() (pyham.taxonomy.Taxonomy method)

get_hog_by_gene() (pyham.ham.Ham method) get_hog_by_id() (pyham.ham.Ham method) get_hog_vis() (pyham.abstractgene.HOG method) get_list_ancestral_genomes() (pyham.ham.Ham method) get_list_extant_genes() (pyham.ham.Ham method) get_list_extant_genomes() (pyham.ham.Ham method) get_list_top_level_hogs() (pyham.ham.Ham method) get_lost() (pyham.mapper.MapLateral method) (pyham.mapper.MapResults method) (pyham.mapper.MapVertical method) get_mrca_taxnode() (pyham.taxonomy.Taxonomy method) get_newick_from_tree() (pyham.taxonomy.Taxonomy method) get_newick_string() (in module pyham.utils) get_node_by_name() (pyham.taxonomy.Taxonomy method) get_number_duplications() (pyham.mapper.MapVertical method) get_number_genes() (pyham.genome.AncestralGenome method) (pyham.genome.ExtantGenome method) (pyham.genome.Genome method) get_number_losses() (pyham.abstractgene.HOG method) get_path_up() (pyham.taxonomy.Taxonomy method) get_retained() (pyham.mapper.MapLateral method) (pyham.mapper.MapResults method) (pyham.mapper.MapVertical method) get_taxon_by_name() (pyham.ham.Ham method) get_top_level_hog() (pyham.abstractgene.AbstractGene method)

H

Ham (class in pyham.ham)

HOG (class in pyham.abstractgene) HOGsMap (class in pyham.mapper)

I

IHAM (class in pyham) InputValidationError (class in pyham.validation) is_child_recursive() (pyham.taxonomy.Taxonomy method)

is_singleton() (pyham.abstractgene.AbstractGene method) (pyham.abstractgene.Gene method) (pyham.abstractgene.HOG method)

M

MapLateral (class in pyham.mapper) MapResults (class in pyham.mapper) MapVertical (class in pyham.mapper) module pyham.taxonomy pyham.TreeProfile pyham.utils pyham.validation

O

ok (pyham.validation.ValidationReport property)

P

ParserFilter (class in pyham.ham) pyham.taxonomy module pyham.TreeProfile module

pyham.utils module pyham.validation module

R

raise_for_errors() (pyham.validation.ValidationReport method)

remove_child() (pyham.abstractgene.HOG method)

S

score() (pyham.abstractgene.HOG method) search_ancestor_hog_in_ancestral_genome() (pyham.abstractgene.AbstractGene method) set_genome() (pyham.abstractgene.AbstractGene method) (pyham.abstractgene.Gene method) (pyham.abstractgene.HOG method)

set_LOFT() (pyham.abstractgene.Gene method) set_taxon() (pyham.genome.Genome method)

T

Taxonomy (class in pyham.taxonomy)

to_ete_tree() (pyham.abstractgene.HOG method) TreeProfile (class in pyham.TreeProfile)

V

validate_input() (in module pyham.validation) ValidationIssue (class in pyham.validation)

ValidationReport (class in pyham.validation) visit() (pyham.abstractgene.HOG method)