Mesquite
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. The primary contributors to the code are Wayne Maddison and David Maddison. It runs on Windows, MacOS, and Linux. More details about Mesquite can be found at Mesquite’s web site.
In addition to the core of Mesquite, David has participated in creating several additional Mesquite packages for various functions. These include:
Zephyr
Zephyr is a Mesquite package written by David and Wayne that provides tools for interacting with phylogeny inference programs including RAxML, IQ-TREE, PAUP*, GARLI, and TNT.
Chromaseq
Chromaseq is a Mesquite package written by David and Wayne integrates the processing of chromatograms within Mesquite. It uses Phred and Phrap to make base calls and contig the data; it allows you to make final base calls in a graphic editor. You can do this with the sequences already integrated into a Mesquite matrix. It provides other functions as well, such as BLASTing to local databases.
Cartographer
The Cartographer package (by, guess who, David and Wayne) allows one to plot the geographic location of taxa onto a calibrated map. This can include plotting a phylogenetic tree onto a map, or just the localities as dots, squares, stars, etc.
DeconMachine
DeconMachine is a python program designed to eliminate contigs from a genomic assembly that are likely contaminants, including those from cross-talk or index hopping. The code was written by James Pflug, with design help from David Maddison.
MacClade
MacClade is a computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts. It had a good life from 1985 through about 2011, but is no longer supported.