Please note this version of msstats is no longer commpatible with current libsequence. I leave hte code up here in case the code to calculate Weir & Cockerham’s Fst is of use, but this code is no longer maintained or supported. Questions about the code should be directed to J. Ross-Ibarra.

This is a modification of K. Thornton’s original msstats program that calculates Weir & Cockerham’s Fst estimator from ms simulations.

You must have libsequence installed for this program to function.

To use msstatsFST with Hudson's ms, try this example:

ms 10 1 -t 2 -I 2 6 4 0 -ej 4 2 1 | msstats -I 2 6 4

which will calculate Fst between two simulated populations of size 6 and 4, respectively.   It should output two lines of stats, one for each pop.  It outputs values of "nan" for all but the final population, which shows the Fst between the two populations. It also works for more than 2 populations, but I cannot remember if the correctness of the calculations for >2 pops has been checked. Please email me for questions or bug reports.
If you use this code, please cite the below papers:

Eckert, A.J., J. van Heerwaarden, J.L. Wegrzyn, C.D. Nelson, J. Ross-Ibarra, S.C. González-Martínez, and D.B. Neale. 2010. Patterns of population structure and environmental associations with aridity across the range of loblolly pine (Pinus taeda L, Pinaceae). Genetics 185: 969-982 Thornton K (2003) libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.

Note that this is NOT an up-to-date version of msstats. Please check the most recent version for msstats for additional changes/bug fixes at the website above.

Original README from msstats:

msstats - read data from ms via stdin, calculate common summary statistics

Copyright (C) 2002 Kevin Thornton

msstats is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA