Basic concepts and vocabulary Mesquite was designed to explore
the evolution of organsims and their characteristics. Here is
some basic vocabulary that relates the biology to the
implementation in Mesquite. - Taxon - One of the basic entities
being studied, usually a species or a gene sequence. In Mesquite
(as in other programs), the word "Taxon" has shifted from its
traditional meaning to become more or less equivalent to
"terminal taxon" (the smallest unit of analysis of
relationships). - Block of taxa - A collection of taxa grouped
together for analysis. In most programs dealing with phylogeny,
there is only a single block of taxa allowed in a file (e.g.,
"Primates", consisting of 20 species of primates). In Mesquite,
multiple blocks are allowed (perhaps to study associations among
them, in the style of Rod Page's programs), and so it is useful
to refer to different blocks of taxa. A block of taxa is
equivalent to a TAXA block in a NEXUS file. - Group Membership
(Taxa partition) - A subdivision of a taxa b