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.
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
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.
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,
Matrix Export (NEXUS), can fuse different matrices
in the course of exporting, create mixed matrices and include
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
A variant on MrBayes Trees is MrBayes Max. A-Post. Tree,
which uses the .p file to find the tree with maximum posterior
Mesquite can call on CLUSTAL
to perform an alignment of a selected region of the matrix.