Comparing sequences

Here, we will compare aligned sequences. We will perform gene and genome-wide comparisons.

Getting ready

We will use DendroPy and will require results from the previous two recipes. As usual, this information is available in the corresponding notebook at 05_Phylo/Comparison.ipynb.

How to do it...

Take a look at the following steps:

1. 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):

   from __future__ import print_function
   import os
   from collections import OrderedDict
   import dendropy
   from dendropy 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...