Index

A | B | C | D | E | F | G | I | L | N | P | R | S | T | U | W

A

add_child() (TreeNode method)
add_face() (FaceContainer method)
(TreeNode method)
add_face_to_node() (in module ete2)
add_feature() (TreeNode method)
add_features() (TreeNode method)
add_sister() (TreeNode method)
AttrFace (class in ete2)

B

build_from_file() (Nexml method)

C

children (TreeNode attribute)
CircleFace (class in ete2)
ClusterNode (class in ete2)
ClusterTree (in module ete2)
convert_to_ultrametric() (TreeNode method)
copy() (TreeNode method)
count_algs() (PhylomeDB3Connector method)
count_trees() (PhylomeDB3Connector method)

D

del_feature() (TreeNode method)
delete() (TreeNode method)
describe() (TreeNode method)
detach() (TreeNode method)
dist (TreeNode attribute)
DynamicItemFace (class in ete2)

E

ete2 (module)
ete2.clustering (module), [1]
ete2.nexml (module)
ete2.parser.seqgroup (module)
ete2.phylo (module)
ete2.phyloxml (module)
ete2.treeview (module)
ete2.webplugin (module), [1]
EvolEvent (class in ete2.phylo)

F

Face (class in ete2)
FaceContainer (class in ete2)

G

get_age() (PhyloNode method)
get_age_balanced_outgroup() (PhyloNode method)
get_algs() (PhylomeDB3Connector method)
get_all_isoforms() (PhylomeDB3Connector method)
get_ascii() (TreeNode method)
get_available_trees_by_phylome() (PhylomeDB3Connector method)
get_best_tree() (PhylomeDB3Connector method)
get_children() (TreeNode method)
get_clean_alg() (PhylomeDB3Connector method)
get_collateral_seeds() (PhylomeDB3Connector method)
get_common_ancestor() (TreeNode method)
get_common_ancestor_OLD() (TreeNode method)
get_descendant_evol_events() (PhyloNode method)
get_descendants() (TreeNode method)
get_distance() (TreeNode method)
get_dunn() (ClusterNode method)
get_entries() (SeqGroup method)
get_external_ids() (PhylomeDB3Connector method)
get_farthest_leaf() (TreeNode method)
get_farthest_node() (TreeNode method)
get_farthest_oldest_leaf() (PhyloNode method)
get_farthest_oldest_node() (PhyloNode method)
get_genome_ids() (PhylomeDB3Connector method)
get_genome_info() (PhylomeDB3Connector method)
get_genomes() (PhylomeDB3Connector method)
get_genomes_by_species() (PhylomeDB3Connector method)
get_go_ids() (PhylomeDB3Connector method)
get_id_by_external() (PhylomeDB3Connector method)
get_id_translations() (PhylomeDB3Connector method)
get_info_homologous_seqs() (PhylomeDB3Connector method)
get_leaf_names() (TreeNode method)
get_leaf_profiles() (ClusterNode method)
get_leaves() (TreeNode method)
get_leaves_by_name() (TreeNode method)
get_longest_isoform() (PhylomeDB3Connector method)
get_midpoint_outgroup() (TreeNode method)
get_my_evol_events() (PhyloNode method)
get_new_phylomedb_id() (PhylomeDB3Connector method)
get_old_phylomedb_ids() (PhylomeDB3Connector method)
get_partitions() (TreeNode method)
get_phylome_algs() (PhylomeDB3Connector method)
get_phylome_info() (PhylomeDB3Connector method)
get_phylome_seed_ids() (PhylomeDB3Connector method)
get_phylome_seed_ids_info() (PhylomeDB3Connector method)
get_phylome_trees() (PhylomeDB3Connector method)
get_phylomes() (PhylomeDB3Connector method)
get_phylomes_for_seed_ids() (PhylomeDB3Connector method)
get_prot_gene_names() (PhylomeDB3Connector method)
get_proteomes_in_phylome() (PhylomeDB3Connector method)
get_raw_alg() (PhylomeDB3Connector method)
get_seq() (SeqGroup method)
get_seq_info_in_tree() (PhylomeDB3Connector method)
get_seq_info_msf() (PhylomeDB3Connector method)
get_seqid_info() (PhylomeDB3Connector method)
get_seqs_in_genome() (PhylomeDB3Connector method)
get_silhouette() (ClusterNode method)
get_sisters() (TreeNode method)
get_species() (PhylomeDB3Connector method)
(PhyloNode method)
get_species_in_phylome() (PhylomeDB3Connector method)
get_species_info() (PhylomeDB3Connector method)
get_tree() (PhylomeDB3Connector method)
get_tree_root() (TreeNode method)

I

ImgFace (class in ete2)
is_leaf() (TreeNode method)
is_monophyletic() (PhyloNode method)
is_root() (TreeNode method)
iter_descendants() (TreeNode method)
iter_entries() (SeqGroup method)
iter_leaf_names() (TreeNode method)
iter_leaf_profiles() (ClusterNode method)
iter_leaves() (TreeNode method)
iter_search_nodes() (TreeNode method)
iter_species() (PhyloNode method)

L

ladderize() (TreeNode method)
link_to_alignment() (PhyloNode method)
link_to_arraytable() (ClusterNode method)

N

Nexml (class in ete2)
NexmlTree (class in ete2)
NodeStyle (class in ete2)

P

PhylomeDB3Connector (class in ete2)
PhyloNode (class in ete2)
PhyloTree (in module ete2)
Phyloxml (class in ete2)
PhyloxmlTree (class in ete2)
populate() (TreeNode method)
ProfileFace (class in ete2)
prune() (TreeNode method)

R

reconcile() (PhyloNode method)
register_action() (WebTreeApplication method)
remove_child() (TreeNode method)
remove_sister() (TreeNode method)
render() (TreeNode method)

S

search_id() (PhylomeDB3Connector method)
search_nodes() (TreeNode method)
SeqGroup (class in ete2)
SequenceFace (class in ete2)
set_default_layout_fn() (WebTreeApplication method)
set_distance_function() (ClusterNode method)
set_external_app_handler() (WebTreeApplication method)
set_external_tree_renderer() (WebTreeApplication method)
set_outgroup() (TreeNode method)
set_seq() (SeqGroup method)
set_species_naming_function() (PhyloNode method)
set_style() (TreeNode method)
set_tree_loader() (WebTreeApplication method)
set_tree_size() (WebTreeApplication method)
set_tree_style() (WebTreeApplication method)
show() (TreeNode method)
sort_descendants() (TreeNode method)
species (PhyloNode attribute)
StaticItemFace (class in ete2)
support (TreeNode attribute)
SVG_COLORS (in module ete2)
swap_children() (TreeNode method)

T

TextFace (class in ete2)
traverse() (TreeNode method)
Tree (in module ete2)
TreeFace (class in ete2)
TreeNode (class in ete2)
TreeStyle (class in ete2)

U

unroot() (TreeNode method)
up (TreeNode attribute)

W

WebTreeApplication (class in ete2)
write() (SeqGroup method)
(TreeNode method)