Below are links to scripts or repositories of scripts I have used in analyses. Most are under continual development. See repositories for more information.
As part of my analysis finding convergent evolution in container specialization in the genus Aedes, I wrote a wrapper script that would perform phylogenetically-informed analysis of variance given several models of evolution.
A set of scripts that take a list of results directories from BUSCO analyses, finds orthologs present in all analyses, outputs orthologs present in some threshold of genomes, aligns all orthologs, and outputs a concatenated multisequence alignment file in Phylip and Nexus formats, with a RAxML partition file and Nexus in file partition scheme.