If we have to find a word to best represent the encounter between informatics and evolutionary biology, that word would definitely be phylogenomics. The large-scale analysis, allowed by the big amount of data made available in the last 20 years, is rapidly imposing the rule that “nothing makes sense in evolutionary biology except in the light of high throughput analysis”. The uptake of the most important evolutionary relationships is subject to large-scale analysis, since the relevant information is often hidden in a mountain of genetic material.
The python module I am going to present is a brand-new module, completely dedicated to phylogenomics, made by Carlos Peña, from the Nymphalidae Systematic Group at the University of Turku (Finland). The package implements several functionalities including blast integration, sequence analysis, fastq- fasta conversions and primer sites finding.
To try it on you python environment you’ll need the modules MySQLdb and biopython installed. Just connect to the pypi page and download the package, then unzip, open the terminal in the unzipped folder and type:
python setup.py build
python setup.py install
Ubuntu users will need to sudo first. For more information check the github page.