Wayne and I have been working hard over the last few weeks to release Mesquite version 3.0, and today we released it!
The main changes in this version of Mesquite are architectural, both in how the user interface is organized, and in how we build and distribute Mesquite. The changes to how we make and distribute Mesquite were done in part to make it much easier to do future releases, and in part to make the code and documentation more open so that others can be involved more easily. We have done this by moving the source code to GitHub, and the documentation to a wiki (http://mesquiteproject.wikispaces.com). In addition, there have been some changes to the files distributed with Mesquite that will make it easier to manage and update.
There are a number of new and useful features in this version of Mesquite, the most important of which is support for a new package called Zephyr.
Zephyr is a package that allows Mesquite to interact with phylogeny inference programs. To begin with we have added support for RAxML, GARLI, and PAUP*, but we will be adding other programs in the future. We released version 1.0 of Zephyr today as well.
Here we are at Pender Harbour, BC, doing the last major push. It was great to do it in such a beautiful location, and it was nice to have our mom there providing support.