Mesquite: A modular system for phylogenetic workflows and analyses
[Download] Current stable release version: 4.01
[New features and bug fixes in this version][YouTube channel with instructional videos]
Mesquite is designed to help phylogenetic and evolutionary biologists organize and analyze comparative data about organisms. Its goal is to provide a "transparent pipeline", giving the user live visualizations of data, trees, and analyses so that they see and understand their data and results as they are being processed.
While early versions of Mesquite emphasized analyses, Mesquite 4 emphasizes data management and coordination of analyses by other programs. It integrates and comes bundled with external programs for tree inference (e.g., IQ-TREE, RAxML), sequencing alignment and trimming (e.g., MAFFT, MUSCLE, trimAl, Spruceup), and other functions.
To see a few of the things Mesquite can do, watch the trailer or the full video below. To learn how to use Mesquite, the manual (with videos) is here
Also, please sign up to the Mesquite Google Group to discuss and ask questions.