This release is version 3.81 of Mesquite, build 955. For more information see http://www.mesquiteproject.org. This fixes some bugs in 3.80, namely a startup problem on macOS, and a few other annoying bugs. Like 3.80, this bundles the Zephyr, Chromaseq, and Cartographer packages into the basic Mesquite download. The core Mesquite also has a few new features beyond v. 3.80.
Because Zephyr, Chromaseq, and Cartographer might be updated independently, you may find newer versions of them at their websites (https://zephyr.mesquiteproject.org, https://chromaseq.mesquiteproject.org, https://cartographer.mesquiteproject.org). The source code available below is just for the core Mesquite packages. The source code for Zephyr, Chromaseq, and Cartographer is available at their respective websites.
Note for Mac OS X users: There are two alternative downloads, one for macOS 10.14 (Mojave) and earlier, and another for OS X 10.15 (Catalina) and later. The difference between the two relates entirely to the security arrangements imposed by Apple; 10.15 and later restricts how programs are distributed. The 10.15 version passes these restrictions, but excludes some convenient alternative methods to run Mesquite. If you are running Mesquite on 10.15 or later, you will need to install the Java Development Kit (JDK) version of Java, not the normal JRE version! Those are available here: https://www.oracle.com/java/technologies/downloads/
Note for Linux users: You may need to use Java 8 (i.e. 1.8). There are bugs in Java 11 to 16 that prevent Mesquite from working. See details on installation web page, and in the instructions in Mesquite_Folder.