Mesquite 4.03 (build 1133)

Mesquite 4.03 is a minor update to Mesquite 4.02, with a few bug fixes and new features, most notably parallelized gene tree inference and ability to assign matrices to groups. 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. Because BLAST is large, we offer downloads below that exclude BLAST.

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: Since 4.03 build 1132 was released on 9 April, two bugs were fixed and released as a new build 1133 on 24 April, in the bundles below. The code attached below and main branch were not updated, but the changes can be found in the development branch. The affected parts are:

• InterpretFasta in mesquite.io.lib
• NameParserOnTaxonNames in mesquite.basic
• TaxonNamesFileProcessor in mesquite.dmanager

Also, MesquiteModule in mesquite.lib was changed, but only to indicate in build number and date.

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.