Introduction+to+Zephyr

=Introduction to Zephyr=

Zephyr is a Mesquite package that allows you to conduct analyses in external phylogenetics programs and have Mesquite automatically harvest the results for you. Zephyr will communicate with GARLI, RAxML, PAUP*, and TNT. Zephyr is primitive in some aspects (for example, there is no elegant way to stop a run in process), but it can still be quite useful. Zephyr also allows you to conduct a SOWH test.

For example, you might start out with a DNA sequence matrix in Mesquite:



With Zephyr installed, and GARLI on your computer, you can then choose Analysis>Tree Inference>Likelihood Tree Inference>GARLI Trees. After choosing a few options in some dialog boxes you will be presented by the main GARLI dialog box in Zephyr:



After making your choices, you then press OK, and Zephyr packages up your data and sends it to a folder that GARLI can access, starts up GARLI, and instructs GARLI of your choices and how to do the search. GARLI then begins searching. This might happen enough behind the scenes that you won't know easily be able to see it happening, except for whatever details are presented in Mesquite.

While GARLI is searching, Zephyr harvest the intermediate results, and presents them to you in a tree window:



When the GARLI run is finished, Zephyr reads the final tree or trees in, and saves them in a tree block within your file:



There are other options, and other features, but this will give you a brief idea of Zephyr's basic features; the SOWH test is described elsewhere.