My brother Wayne is visiting, and we are making very good progress on Zephyr. Programming is especially appealing when the outside world is covered in quiet snow.
Zephyr is a package for Mesquite that links Mesquite to phylogeny inference programs. For example, one can have a matrix of DNA sequences in Mesquite, and ask that GARLI finds the maximum likelihood tree. A dialog box from Zephyr pops up with GARLI settings, you choose them, and then Zephyr starts up GARLI. As GARLI is running, Mesquite/Zephyr is monitoring its progress, and showing you the trees live in a tree window in Mesquite. Once GARLI is done, Mesquite harvests the trees or trees and stores them in the current project.
Below is a view of Mesquite with GARLI running in the background (in the black terminal window at right), and the latest GARLI tree shown in the tree window. As GARLI runs, one can watch that tree being continually adjusted. (Touch on the image below to see a larger version of it.)
We’ve been using Zephyr for a few years in our own work, and are now putting the effort in to making it usable by others. So far it enables one to run GARLI, RAxML, TNT, and PAUP from within Mesquite, although the options for TNT and PAUP are limited.
We’re very pleased with the progress we’ve made, and hopefully will have something available for folks in the spring sometime.
(By the way, the image on the Zephyr banner is a closeup of the elytron of Bembidion zephyrum, one of my favorite beetles. It lives on the sandy beaches of the Pacific Ocean in western North America.)