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README.txt
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===========================================================
SweeD
===========================================================
Copyright (C) 2012 Pavlos Pavlidis and Nikolaos Alachiotis
SweeD implements a maximum-likelihood approach to detect selective sweeps
using the site frequency spectrum.
The sequential version of SweeD represents an algorithmically improved re-design
of the SweepFinder tool by Nielsen et al. (2005).
For more details see:
R. Nielsen, S. Williamson, Y. Kim, M.J. Hubisz, A.G. Clark, and C. Bustamante,
"Genomic scans for selective sweeps using SNP data", Genome Research, pages 1566-1575, 2005.
Linux Platforms
---------------
Compile:
make -f Makefile.gcc
Execute:
./SweeD -name TEST -input TEST.SF -grid 10000
Windows Platforms
-----------------
No Windows version is yet available.
Change Log
----------
March 2014: SweeD v3.2.4 (it can read the ms-like output of msABC)
October 2013: SweeD v3.2.1 (fixed bug in VCF format associated with ALT state as '.')
January 2013: SweeD v3.1 (fixed bug in VCF parser associated with the handling of missing data)
November 2012: SweeD v3.0 (analytical calculation of SFS)
November 2012: SweeD v2.6 (fixed bug in multiple SFS input file)
October 2012: SweeD v2.5 (checkpointable)
October 2012: SweeD v2.0 (scalable for more than 1000 sequences, parallel)
September 2012: SweeD v1.0
Contact
-------
Pavlos Pavlidis - [email protected]
Nikos Alachiotis - [email protected]
This program is free software; you may redistribute it and/or modify its
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.