ClipKIT
A fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.
BioKIT
A versatile toolkit for processing or conducting analyses on alignments, coding sequences, fastq files, and genome files
OrthoSNAP
Command-line tool for increasing the size of molecular evolution datasets that can then be used for diverse studies including phylogenomics and genome-wide surveys of positive selection
orthofisher
Automated HMMsearches among a set of proteomes using a predetermined set of orthologs. Sequence similarity searches classify results as multi-copy, single-copy, or absent in a given genome
treehouse
Sometimes phylogenies are so large it is challenging to determine the relationships among a subset of taxa. To remedy this issue treehouse allows users to obtain subtrees from larger phylogenies
ggpubfigs
R package with customized themes and colorblind friendly color palettes to help create publication (or presentation) ready figures