Comparing sequences

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

Getting ready

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 Chapter07/Comparison.py.

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 data from two other species of the genus Ebola virus that are available in the extended dataset, that is, the Reston virus (RESTV) and the Sudan virus (SUDV):

   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...