Take a look at the following steps:
- Let's start analyzing the gene data. For simplicity, we will only use the data from two other species of the genus Ebola virus that are available in the extended dataset: the Reston virus (RESTV) and the Sudan virus (SUDV):
import osfrom collections import OrderedDictimport dendropyfrom dendropy.calculate import popgenstatgenes_species = OrderedDict()my_species = ['RESTV', 'SUDV']my_genes = ['NP', 'L', 'VP35', 'VP40']for name in my_genes: gene_name = name.split('.')[0] char_mat = dendropy.DnaCharacterMatrix.get_from_path('%s_align.fasta' % name, 'fasta') genes_species[gene_name] = {} for species in my_species: genes_species[gene_name][species] = dendropy.DnaCharacterMatrix() for taxon, ...
