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. Additionally, 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:
conda install –c bioconda mafft trimal muscle=3.8
As usual, this information is available in the corresponding Jupyter Notebook file at Chapter07/Alignment.py. You will need to run the previous notebook beforehand, as it will generate the files that are required here. In this chapter, we will use Biopython.
How to do it...
Take a look...
