This continues with the basics of using Mesquite. A single project in Mesquite can have multiple blocks of taxa. Each block of taxa can have multiple character matrices. Each character matrix is linked to a particular block of taxa, and a matrix can be accessed only for calculations that concern its block of taxa. Also, information in separate projects cannot communicate. This means that to incorporate information from a separate file, that file needs to be included or linked to the current project. Examples are given of what can go wrong. For version 2.75.

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