This snakemake file contains a workflow allowing the creation of MAFFT alignments and RAxML phylogenies. Inputs can either be a set of amino acid or nucleotide sequences. It is coded for use with a snakemake configuration by RomainFeron, so that it works with a computing cluster managed by SLURM. Note that the outgroups in the ProteinTree and GeneTree rules need to be changed to accomodate your dataset.
Contains the amino acid and CDS sequences of the sex determination gene doublesex in Aedes aegypti, Drosophila melanogaster and 13 Anopheles species. Male and female transcripts are present within each. This was the original dataset the workflow was tested on when I made it.