Mesquite 3.81 (build 955)

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.

Mesquite 3.80 (build 950)

This release is version 3.80 of Mesquite, build 950. For more information see http://www.mesquiteproject.org. The biggest change from v. 3.7 is the bundling of the Zephyr, Chromaseq, and Cartographer packages into the basic Mesquite download. The core Mesquite also has a few new features and bug fixes beyond v. 3.7.

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 11-16 that prevent Mesquite from working. See details on installation web page, and in the instructions in Mesquite_Folder.

Mesquite 3.70 (Build 940)

This release is version 3.70 of Mesquite, build 940. For more information see http://www.mesquiteproject.org. It has a few new features and bug fixes beyond v. 3.61. The biggest fixes are in the executables, to allow Mesquite to start under more recent versions of Java.

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; 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 will likely need to use Java 8 (i.e. 1.8). There are bugs in Java 11-16 that prevent Mesquite from working. See details on installation web page, and in the instructions in_Mesquite Folder.

Mesquite 3.61 (Build 927)

This is release version 3.61 of Mesquite, build 927. For more information see http://www.mesquiteproject.org. It has a few new features and bug fixes beyond v. 3.60.

Note for Mac OS X users: There are three alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for MacOS 10.10 (Yosemite) to 10.14 (High Sierra), and another for OS X 10.15 (Catalina). The difference between the first two is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10-10.14 version uses Java 1.7 or above. In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled. However, neither of those versions will run directly on Mac OS X 10.15 Catalina (or later). If you are using Catalina, choose Mesquite 3.61-MacOSX-10.15Catalina or higher.dmg.

If you already have Mesquite 3.61 installed, and are only looking to correct the problem with the app file not working on MacOS 10.15 (Catalina), you can download just the new executable (MesquiteByScriptExecutable.dmg) and follow the instructions there.

The new Catalina executable MesquiteByScript.app has drawbacks: there is a delay on startup, and you can't open files by dropping files onto the icon after Mesquite has already started (you can do this when you first start up Mesquite).

An alternative for Catalina users that allows you to use the old Mesquite.app requires that you download two versions and move some files around. Here's how you'd do it (we'll explain why below):

• Download the version of Mesquite for Java 1.7 and above
• Move the Mesquite Folder in that dmg file onto your hard disk, and open up the folder. Find the Mesquite app file (the one with the Mesquite icon), and throw it away.
• Go to https://github.com/MesquiteProject/MesquiteCore/releases/tag/v3.6
• Download Mesquite.3.6-MacOSX.10.10.or.higher-Java-1.7plus.dmg
• Open up that dmg, and open up the Mesquite Folder in it.
• Take the Mesquite app file from there and move it into the Mesquite Folder on your hard disk. That is, you are replacing the Mesquite app file from the latest version with the app file from version 3.6
• Now start up Mesquite from that app file

If you're wondering why we can't simply make a version that has the older Mesquite.app file, the key is that Catalina's new security system gives special forgiveness to old dmg files, and we can't create an old dmg file without a time machine.

Mesquite 3.6 (Build 917)

This version of Mesquite adds several minor new features, as well as compatibility with Zephyr 3.0 (supporting SSH-based communication) and Chromaseq 1.5 (with easier GenBank submission).

Mesquite 3.51 (build 898)

This is release version 3.51 of Mesquite, build 898. For more information see http://www.mesquiteproject.org. It has a few bug fixes beyond v. 3.50.

Note for Mac OS X users: There are two alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for macOS 10.10 (Yosemite) and higher. The difference is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10+ version uses Java 1.7, 1.8 or 9. In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled.

Mesquite 3.50 (build 888)

This is release version 3.50 of Mesquite, build 888. For more information see http://www.mesquiteproject.org. It has a few bug fixes and workarounds and an offline manual.

Note for Mac OS X users: There are two alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for OS X 10.10 (Yosemite) and higher. The difference is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10+ version uses Java 1.7, 1.8 or 9. In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled.

Mesquite 3.40 (build 877)

This is release version 3.40 of Mesquite, build 877. For more information see http://mesquiteproject.wikispaces.com. It has a few bug fixeds and enhancements, and is now compatible with Java 9.

Note for Mac OS X users: There are two alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for OS X 10.10 (Yosemite) and higher. The difference is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10+ version uses Java 1.7, 1.8 or 9. In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled.

Mesquite 3.31 (build 859)

This is release version 3.31 of Mesquite, build 859. For more information see http://mesquiteproject.wikispaces.com. Build 859 fixes a bug in installing extra packages. Version 3.31 build 858 was a minor update to 3.30, with a few enhancements, but primarily to solve a bug in interaction with alignment programs under older versions of Java.

Note for Mac OS X users: There are two alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for OS X 10.10 (Yosemite) and higher. The difference is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10+ version uses Java 7 or 8 (also known as Java 1.7 or 1.8). In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled.

Note for all users: Mesquite 3.31 and older versions will likely not work with Java 1.9.

Mesquite 3.31 (build 858)

This is release version 3.31 of Mesquite, build 858. For more information see http://mesquiteproject.wikispaces.com. It is a minor update to 3.30, with a few enhancements, but primarily to solve a bug in interaction with alignment programs under older versions of Java.

Note for Mac OS X users: There are two alternative downloads, one labelled as being for OS X 10.9 (Mavericks) and lower, one labelled as being for OS X 10.10 (Yosemite) and higher. The difference is that the 10.9 version uses Java 6 (also known as Java 1.6), and the 10.10+ version uses Java 7 or 8 (also known as Java 1.7 or 1.8). In fact, you can use either Mesquite version for either operating system version (depending on the Java version you have installed), but we recommend them for the operating systems as labelled.

Note for all users: Mesquite 3.31 and older versions will likely not work with Java 1.9.