What is MigraPhyla?

MigraPhyla 1.0b tabulates migration events through a phylogeny inferred by parsimony and by Monte Carlo simulation identifies migration pathways with traffic greater than expected by chance. The program is currently less a standard application than a jury-rigged collection of procedures across platforms. The user is forewarned: The program is not the most user friendly at this point and requires changes to the code for every new analysis. We have only begun the process of compiling all the modules into a single platform with dropdown menus and input boxes.

How do I install MigraPhyla?

For installation we suggest you first make a "MigraPhyla" folder on your computer desktop. To download the MigraPhyla routines click here. When extracting the files into the MigraPhyla folder, select “All folders/files in the archive”.

The resulting WinZip file contains a PDF of the MigraPhyla manual, as well as JAVA files for generating PAUP* input, for summing up migration events in PAUP* output, for conducting the Monte Carlo test, and for identifying the maximum value for each migration pathway across the Monte Carlo trials.You will also find here Excel files showing sample migration and probability matrices, as well as a sample sparse false discovery rate correction for the Monte Carlo P values.

Who's responsible?

MigraPhyla's code was written by HoangMinh HoDac and Richard Lathrop in Fall 2005 with consultation from Walter Fitch and Rob Wallace. Wallace developed the Excel files. Wallace and HoDac wrote the documentation. The code was written for the work described in

Wallace RG, HM HoDac, R Lathrop, and WM Fitch. 2007. A statistical phylogeography of influenza A H5N1. Proceedings of the National Academy of Sciences. 104:4473-4478.

Wallace RG and WM Fitch. Influenza A H5N1 immigration is filtered out at some international borders. Under review.

Bug alerts and suggestions are appreciated.

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