(updated February 2001)
At any given time Mesquite is using information about taxa, characters and so on. This information might consist of:
Each of these is an element of information. Each corresponds roughly to a single block or command in a NEXUS file. Such an element can be created at the user's command. For instance, a command requesting a new data matrix might yield a blank matrix the user can fill in. An element might also be read from a file on disk, as happens when Mesquite reads in a NEXUS data file.
Since Mesquite is designed to use the NEXUS file format (Maddison, D.R., D.L. Swofford, and W.P. Maddison. 1997. NEXUS: An extensible file format for systematic information. Systematic Biology 46: 590-621) as its primary file format, we will assume for the moment that it is using NEXUS files. A typical NEXUS file might contain a TAXA block defining taxa, a CHARACTERS block giving character data, and a TREES block. After Mesquite reads in the file, Mesquite will have in its memory a list of taxa (that it got from the TAXA block), a data matrix (that it got from the CHARACTERS block), and a set of trees (from the TREES block).
However, Mesquite is not limited to NEXUS files with this set of three blocks. Mesquite is happy with files with more than one TAXA block, more than one CHARACTERs block and so on.
Mesquite can read such a file from a web server if given the URL. If run as a local application, Mesquite can read such a file from the user's computer.
Since Mesquite can accumulate and analyze a more or less indefinitely large collection of elements of information (several sets of taxa, data matrices, and so on), Mesquite doesn't need to respect the boundaries of files. That is, it could read a TAXA block from one file on the disk, and read a data matrix for those taxa from another file on disk, and a set of trees from another file. While other programs can handle external treefiles or command files, Mesquite can handle external character matrices, assumptions, and so on.
Mesquite therefore makes a distinction between the collection of elements of information that are currently interacting with one another in Mesquite's calculations, and the physical files on disk or server. The former collection, which may include information gathered from several files, is called a project. The set of files to which the elements of information in a project belong are said to be linked.
Mesquite shows a list of the projects and files currently active in the Projects and Files window:
In Mesquite there are three ways to read a file: Open, Include and Link.