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.