Here, we will compare aligned sequences. We will perform gene and genome-wide comparisons.
We will use DendroPy and will require the results from the previous two recipes. As usual, this information is available in the corresponding Notebook at Chapter06/Comparison.ipynb
.
Take a look at the following steps:
import os from collections import OrderedDict import dendropy from dendropy.calculate import popgenstat genes_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...