Rosenberg lab at Stanford University


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 2.0]
[Download article 1: arbitrary species trees (PNAS 113: 8002-8009)]
[Download article 2: 3 and 4 taxon calculations (TPB 129: 133-147)]
[Download article 3: arbitrary numbers of groups, arbitrary species trees]

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
./ inputfile.txt
or simply
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
December 6, 2017 - upload of new version of the manual with trivial changes; replacement of the linux version to include a missing library
February 28, 2022 - upload of version 2.0 of the software