Before we can perform any phylogenetic analysis, we need to align our genetic and genomic data. Here, we will use MAFFT (http://mafft.cbrc.jp/alignment/software/) to perform the genome analysis and the gene analysis will be performed using MUSCLE (http://www.drive5.com/muscle/).
To perform the genomic alignment, you will need to install MAFFT, and to perform the genic alignment, MUSCLE will be used. Also, we will use TrimAl (http://trimal.cgenomics.org/) to remove spurious sequences and poorly aligned regions in an automated manner. On Ubuntu and Linux, MAFFT and MUSCLE can be installed using apt-get install mafft muscle packages. TrimAl will have to be manually installed.
As usual, this information is available in the corresponding notebook at 05_Phylo/Alignment.ipynb. You will need to have run the previous notebook as it will generate files that are required here.
In this chapter, we will use Biopython.