Aligning genetic and genomic data

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. The gene analysis will be performed using MUSCLE (http://www.drive5.com/muscle/).

Getting ready

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. All packages are available from Bioconda. As usual, this information is available in the corresponding Jupyter Notebook file at Chapter06/Alignment...