Mesquite is a very popular modular software for comparative evolutionary analyses involving phylogenies, one that I have used for a long time and actually like a lot.
A couple of weeks ago, in response to a reviewer who asked for me to use the latest version of Mesquite, version 2.75, instead of 2.74 (which I used for the analyses in the ms), I recently updated Mesquite to build 556. Then, yesterday, I realized that I had deleted a couple of module folders (e.g. PDAP) from the “mesquite” folder during the aforementioned upgrade. So, I attempted to simply go to Mesquite and download these modules again. Unfortunately, my attempts failed.
I tried to access a couple of different pages on the website yesterday and today, to no avail. The site, http://mesquiteproject.org, and all of its pages fail to load. Thus, I assume this means that the site is undergoing maintenance, perhaps related to a new release of the program. But be advised that you will not be able to download Mesquite or read content from mesquite.org at present!! This also carries over into checks for notices/installs. If you open Mesquite and click File > Check Now for Notices/Installs and specify the default URL (http://mesquiteproject.org/mesquite/notice/notices.xml), then you will get a wonderful note saying, “Sorry, no relevant information found at that URL.” Of course, the funny thing is that this is the only website that we expect to always contain useful information on this point.
Fortunately, I found one of my flash drives had the full 2.74 Mesquite folder, with all of my special module folders. So, all I did was simply copy the folder I needed back onto my mac, and voila!, no problems… I went on happily with my analyses.
However, the question remains, when will the Mesquite guys get the website back up… today, tomorrow, next week? As much as I love this program, perhaps next time the Mesquite gurus could set up a mirror site, or at least a site explaining that mesquite.org is closed for maintenance. Please let me know if there is another way to deal with this problem.