Rosenberg lab at Stanford University

Monophyler

Monophyler computes the probability of monophyly of a specified set of gene lineages conditional on a species tree. Monophyler uses the coalescent together with an arbitrary species tree to determine the monophyly probability for a set of lineages or the reciprocal monophyly probability for a pair of sets of lineages. It can also accommodate various computations involving three or four lineage sets.

[Download software package] (you will be directed first to a registration page and we would very much appreciate if you register)
[Download manual]
[Download article (Proceedings of the National Academy of Sciences 113: 8002-8009)]

To use the UNIX versions, unzip and untar the files in an appropriate directory using

gunzip filename.tar.gz; tar xvf filename.tar
where "filename.tar.gz" is the downloaded file. Run the program in UNIX by typing
./monophyler_linux.sh inputfile.txt
or simply
./monophyler_linux.sh
to start the graphical user interface.

Please send comments or problems with Monophyler to Rohan Mehta.


Software history

April 5, 2016 - upload of peer review version of the software
July 26, 2016 - upload of version 1.0 of the software