Interaction with Other Programs

Mesquite needs to be able to interact with various other programs because typically it depends on them for inference of phylogenetic trees. The programs can interact through sharing files, or in a few cases directly.

Importing/exporting files

Mesquite by default currently uses the NEXUS format for files. Other programs such as MacClade, PAUP, MrBayes and NDE all deal with NEXUS files, but there may be some commands not handled by all programs. Mesquite has in addition importers and exporters for various other file formats. You can import a file by requesting to open it; Mesquite will ask you to identify its file format. You can export a file using the Export item in the File menu.

MacClade — MacClade may not be able to read all of the information in a NEXUS file written by Mesquite, especially if it has multiple character or taxa blocks. You may need to simplify the file (e.g. delete some taxa blocks) for it to be read. Also, you could export the file as a Simplified NEXUS file for reading by MacClade.

PAUP* — You might want to change PAUP's setting to "Issue Warning and continue" under "Warnings & errors" (set errorstop = no) so that PAUP does not complain about IDs commands within taxa blocks. Another alternative is to export the file as a Simplified NEXUS file.

NDE — NDE currently cannot handle some commands in the NEXUS files that Mesquite may write, including the TITLE command. If NDE warns you about this, turn off Mesquite's TITLE commands using the menu item under Defaults in the File menu.

CLUSTAL — You may find it useful to use Alternative Taxon Names and then Condense Taxon Names before exporting files for use by CLUSTAL, for it has difficulty with punctuation and long names.

MrBayes interactions

There are two special file exporters useful for work with MrBayes: first, there is an exporter Export NEXUS for MrBayes that uses a simplified NEXUS format. It also composes a MrBayes block that includes character partitioning. A second exporter, Fused Matrix Export (NEXUS), can fuse different matrices in the course of exporting, create mixed matrices and include MrBayes blocks.

There is a special Tree Source (MrBayes Trees...) that can read a MrBayes tree file as MrBayes is producing it. If the option is so set, Mesquite can respond to new trees being added to the file. Thus, if you have a chart showing a value (say, Felsenstein's contrast correlation) over trees coming in from a MrBayes analysis, the chart will get updated when a new tree is added. In the Tree window you can also ask to retrieve only the last tree in the file, and this will update as new trees are added. If MrBayes' .p files are in the same directory as its .t files, then MrBayes Trees will attach to the trees the tree score from MrBayes. This will be available as a NumberForTree "MrBayes Score".

A variant on MrBayes Trees is MrBayes Max. A-Post. Tree, which uses the .p file to find the tree with maximum posterior probability.

CLUSTAL

Mesquite can call on CLUSTAL to perform an alignment of a selected region of the matrix.