Mesquite 4.02 (build 1109)

Mesquite 4.02 is a minor update to Mesquite 4.01, with a few bug fixes and new features, most notably Codon alignment for DNA matrices. Speed has been considerably improved for some operations with data files with 1000s of loci (file reading, Parallel Alter Matrices, deconcatenation of large concatenated alignment). See here for a more information about changes.

Mesquite 4 is a major upgrade over 3.x, with many new features big and small. There are new ways to build workflows and manage taxa, characters, and trees. It is able to handle phylogenomic datasets, tested to 150 taxa X 3500 matrices totalling more than 2,000,000 sites. The interface has many improvements, including new tools and actions from right-clicking, and many convenience and productivity features. It has much faster and cleaner graphics under Windows, and Linux's Java crashes have been resolved. There are many bug fixes. For more information and videos of some of the new features see https://www.mesquiteproject.org and our YouTube channel https://www.youtube.com/channel/UCfSmgC0O_dWLI0PEoXZbS4Q.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer. IQ-TREE, RAxML, MAFFT, MUSCLE, BLAST, trimAl, and Gblocks are bundled with and integrated into Mesquite.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

Please come join us at the Mesquite Google Group (https://groups.google.com/g/mesquite-project) to discuss and ask questions.

Addendum: Below is a patch for a bug that causes a crash when characters are deleted from categorical morphological data matrices with annotations for character states (in the State Names Editor). Instructions are included.

Mesquite 4.01 (build 1092)

Mesquite 4.01 is a minor update to Mesquite 4, with one substantive bug fix, some small bug fixes and interface improvements, and a few new features — NINJA for neighbor joining, node spots for decorating the tree, and new options to merge taxa. The fixed substantive bug involved improperly sequence trimming after inverting highlights after showing trimming/flagging via Color Matrix Cells.

Mesquite 4 is a major upgrade over 3.x, with many new features big and small. There are new ways to build workflows and manage taxa, characters, and trees. It is able to handle phylogenomic datasets, tested to 150 taxa X 3500 matrices totalling more than 2,000,000 sites. The interface has many improvements, including new tools and actions from right-clicking, and many convenience and productivity features. It has much faster and cleaner graphics under Windows, and Linux's Java crashes have been resolved. There are many bug fixes. For more information and videos of some of the new features see https://www.mesquiteproject.org and our YouTube channel https://www.youtube.com/channel/UCfSmgC0O_dWLI0PEoXZbS4Q.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer. IQ-TREE, RAxML, MAFFT, MUSCLE, BLAST, trimAl, and Gblocks are bundled with and integrated into Mesquite.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

Please come join us at the Mesquite Google Group (https://groups.google.com/g/mesquite-project) to discuss and ask questions.

Note: there is a bug in writing PDF files in Mesquite 4 that can be fixed by downloading the file "Patch.to.correct.PDF.file.writing.zip", unzipping the file, and following the instructions therein.

Mesquite 4.0 (build 1086)

This major update to Mesquite is version 4.0, build 1086. There are many new features, both big and small. There are new ways to build workflows and manage taxa, characters, and trees. It is able to handle phylogenomic datasets, tested to 150 taxa X 3500 matrices totalling more than 2,000,000 sites. The interface has many improvements, including new tools and actions from right-clicking, and many convenience and productivity features. It has much faster and cleaner graphics under Windows, and Linux's Java crashes have been resolved. There are many bug fixes. For more information and videos of some of the new features see http://www.mesquiteproject.org.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer. IQ-TREE, RAxML, MAFFT, MUSCLE, BLAST, trimAl, and Gblocks are bundled with and integrated into Mesquite.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

Please come join us at the Mesquite Google Group (https://groups.google.com/g/mesquite-project) to discuss and ask questions.

Mesquite 4 beta #2 (build 1076)

This is a second beta test (pre-release) of version 4 of Mesquite, build 1076, with many new features over version 3.x, especially for phylogenomics. Videos of new features are available via the Mesquite Home page: https://www.mesquiteproject.org/.

Please give feedback as to how it is working for you via the Mesquite Google Group: https://groups.google.com/g/mesquite-project. There is a list of known issues here: https://htmlpreview.github.io/?https://github.com/MesquiteProject/MesquiteCore/blob/development/knownIssues.html.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

Beta2 has much faster reading of files with thousands of matrices (e.g., for phylogenomics). It has several refinements and new features since the first 4.beta, including Trace All Changes (known from MacClade) and Import GenBank Numbers.

Mesquite 4 beta (build 1073)

This is a beta test (pre-release) of version 4 of Mesquite, build 1073, with many new features over version 3.x, especially for phylogenomics. Videos of new features are available via the Mesquite Home page: https://www.mesquiteproject.org/.

Please give feedback as to how it is working for you via the Mesquite Google Group: https://groups.google.com/g/mesquite-project. There is a list of known issues here: https://htmlpreview.github.io/?https://github.com/MesquiteProject/MesquiteCore/blob/development/knownIssues.html.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

This build is almost identical to build 1072, and for macOS and Windows users will behave almost identically. However, for Linux users it solves the Linux graphics crashes.

Mesquite 4 beta (build 1072)

This is a beta test (pre-release) of version 4 of Mesquite, build 1072, with many new features over version 3.x, especially for phylogenomics. Videos of new features are available via the Mesquite Home page: https://www.mesquiteproject.org.

Please give feedback as to how it is working for you via the Mesquite Google Group: https://groups.google.com/g/mesquite-project. There is a list of known issues here: https://htmlpreview.github.io/?https://github.com/MesquiteProject/MesquiteCore/blob/development/knownIssues.html.

Bundled with Mesquite are the extra packages Zephyr, Chromaseq, and Cartographer.

This requires a recent version of Java. We recommend JDK 21 or better from Oracle, available here: https://www.oracle.com/java/technologies/downloads/

We offer a Linux version, but please note that in our testing it has some serious issues, due to an apparent bug in Oracle's Java. See the Known Issues page linked above.

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.