Programs below, written in C, were initially developed for Unix (Linux, OS X) machine.  After downloading , extract tar files (tar -xf *.tar)

1. Programs for simulating and detecting signatures of selective sweep on DNA sequence data (download the package [KimCLA0908.tar])

**Updated 9/3/06: a serious bug in ssw was fixed:  in the previous versions, incorrect outputs were generated for fixed S (given number of  polymorphic sites) simulations. This error caused segregating patterns of some sites overwritten by those of other sites.

**Updated 9/22/08: Two bugs, one related to memory allocation and the other related to the calculation of GOF, in CLsw.c were found and corrected (Thanks to Simon Boitard (Toulouse) and James Cai (Stanford)).

    - See instruction in CLmanualv2.pdf

    - Dr. Haipeng Li [li@zi.biologie.uni-muenchen.de] in University of Munich compiled the program in Windows XP and told me it runs ok: For Microsoft C/C++ compiler

        cl ssweep.c -o ssw

        cl -c CLsw.c
        cl -c minfunc.c
        cl -o clsw CLsw.obj minfunc.obj 

2. Programs for the composite likelihood analysis of selective sweeps using 2-locus sampling probabilities (download the package [TwoLocus.tar])

    - See instruction in Instruction.txt (ref. Kim and Nielsen 2004, Genetics 167:1513)

3. Programs for the composite likelihood analysis of incomplete selective sweeps (package, instruction)

    - Ref: Meiklejohn et al. 2004, Genetics 168: 265.

There are many other C codes that perform simulations/calculations mentioned in my publications. I'm too lazy to put all of them here. But they are available upon request.

Questions: yuseob.kim@asu.edu