Bioinformatics with Python Cookbook - Second Edition

How to do it...

Take a look at the following steps:

1. We will now run MAFFT to align the genomes, as shown in the following code. This task is CPU-intensive and memory-intensive, and will take quite some time:

from Bio.Align.Applications import MafftCommandlinemafft_cline = MafftCommandline(input='sample.fasta', ep=0.123, reorder=True, maxiterate=1000, localpair=True)print(mafft_cline)stdout, stderr = mafft_cline()with open('align.fasta', 'w') as w:    w.write(stdout)

The parameters are the same as the ones specified in the supplementary material of the paper. We will use the Biopython interface to call MAFFT.

2. Let's use trimAl to trim sequences, as follows:

os.system('trimal -automated1 -in align.fasta -out trim.fasta -fasta')

Here, we just ...