Yesterday, after about three years in gestation, we released Zephyr 2.0.  Zephyr is a Mesquite package that manages interactions with phylogeny inference packages including RAxML, GARLI, PAUP, and TNT.

The most notable additions to Zephyr 2 include implementation of the SOWH test, CIPRes support, much better interapplication communication, and more extensive support for PAUP.   Many bugs were also fixed, and other improvements made.

SOWH Test

The Swofford-Olsen-Waddell-Hillis test allows one to test particular aspects of phylogenetic structure, such as the presence of a hypothesized clade. Given a Mesquite file containing:

• the data matrix
• a constraint tree showing just the phylogenetic structure to be tested (e.g., a tree showing just the one clade with everything else as polytomies)
• the model tree: the best tree with branch lengths that fits that constraint (inferred in a constrained analysis)
• models of evolution (e.g., GTR+I+G) with parameter values inferred from the matrix,

then the SOWH feature in Mesquite will automatically find the observed value of the test statistic using whatever tree inference program you choose among those Zephyr supports, and simulate data many times on the model tree, calculating the test statistic for each simulated matrix.  It will show you the p-value as the analyses goes along, and gives a report once you have decided you have done enough replicates.

In the figure above, the model tree on which data are simulated is shown in the middle, with the results from the SOWH test on the right.  (In this example, only four replicates were conducted; to get an accurate estimation of the p-value, many more would need to be done.)

More details are in Zephyr’s SOWH test documentation.

CIPRes connectivity

CIPRes (CyberInfrastructure for Phylogenetic Research, http://phylo.org) provides a gateway for doing phylogenetic inference on a fast cluster of computers.  Zephyr 2 allows one to run analyses on CIPRes from within a Mesquite session, and will harvest the results once done and move the trees into the Mesquite file.

Interapplication communication

Zephyr 2 has many improvements under the hood, including much better communication mechanisms between Mesquite and the external program.  Among the improvements are the option to have Mesquite directly start the external program (as opposed to asking the operating system’s shell to do that), which gives Mesquite more control over the process.

Better PAUP support

Zephyr 2 now provides a means to do likelihood, distance, and SVD quartets analyses using PAUP from within Mesquite.