Package ete2 :: Package phylomedb :: Module phylomeDB

Module phylomeDB

Classes

PhylomeDBConnector
Reuturns a connector to a phylomeDB database.

Variables

__VERSION__ = 'ete2-2.0rev94'
'phylomedb' provides an access API to the data stored in the phylogenetic database PhylomeDB *[1].

ROOTED_PHYLOMES = {1: {'Aga': 8, 'Ago': 9, 'Ame': 8, 'Ath': 10...

__package__ = 'ete2.phylomedb'

Variables Details

[hide private]

VERSION


'phylomedb' provides an access API to the data stored in the
phylogenetic database PhylomeDB *[1].

All methods to perform queries are implemented within the
PhylomeDBConnector class.

 *[1] PhylomeDB: a database for genome-wide collections of gene
 phylogenies Jaime Huerta-Cepas, Anibal Bueno, Joaquin Dopazo and Toni
 Gabaldon.

      PhylomeDB is a database of complete phylomes derived for
      different genomes within a specific taxonomic range. All
      phylomes in the database are built using a high-quality
      phylogenetic pipeline that includes evolutionary model testing
      and alignment trimming phases. For each genome, PhylomeDB
      provides the alignments, phylogentic trees and tree-based
      orthology predictions for every single encoded protein.

Value:

'ete2-2.0rev94'

ROOTED_PHYLOMES

Value:

{1: {'Aga': 8,
     'Ago': 9,
     'Ame': 8,
     'Ath': 10,
     'Bta': 3,
     'Cal': 9,
     'Cbr': 8,
     'Cel': 8,
...