Interactions+with+Other+Programs

=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.

Direct interactions with RAxML, GARLI, PAUP*, and TNT
If you wish to have the ability to have RAxML, GARLI, PAUP*, and TNT run from within Mesquite, with Mesquite monitoring the analysis and harvesting the results at the end, you may wish to consider installing the Zephyr package.

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. You may find it helps to turn off Mesquite's TITLE commands using the menu item under Defaults in the File menu. 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.

MrBayes interactions
There are two special file exporters useful for work with MrBayes: first, there is an exporterExport 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.

Mesquite can also read the tree files produced by **MrBayes's sumt** command. This allows you to visualize the values on branches, such as the Bayesian Posterior Probability saved into the tree description by MrBayes. To do this, you will need to open the file using the File>Open Other>**Special NEXUS** ... command, and ask when queried to using the "Import MrBayes Consensus Tree File" feature. This will tell Mesquite that the trees being read in are annotated using MrBayes extensions to the tree description format. To see the values for each node, go to a treewindow displaying the tree, and choose either Display>Node-Associated Values>Choose Values to Show (which will give you the choice to show "prob" (the Bayesian Posterior Probability), "probstddev", "lengthmean", and "lengthmedian"), or Display>Node-Associated Text>Choose Associated Text to Show (with will give you the choice to show "probrange", "prob+-sd", or "length95%HPD"). You may wish to turn off drawing of the values on the terminal branches, by unchecking "Show on Terminal Branches" in the Node-Associated Values or Node-Associated Text menu items.

Alignment Programs
Mesquite can call on MAFFT, Muscle, or CLUSTAL to conduct an alignment of a selected region of the matrix. Y ou may find it useful to use Alternative Taxon Names and Condense Taxon Names before using an alignment program, for they may difficulty with punctuation or long names.