Software

Statistical Genetics

Hotspotter

Hotspotter implements the PAC (Products of Approximate Conditional) model for estimating recombination rate (Li and Stephens, 2003). (Documentation (PDF), ChangeLog)

hotspotter-1.2.1.tar.bz2 (130 KB, SIG): source code.
hotspotter-1.2.1-i386-linux.tar.bz2 (1200 KB, SIG) : precompiled executables for GNU/Linux i386, statically linked and compressed with UPX.
hotspotter-1.2.1-ppc-darwin.tar.bz2 (898 KB, SIG): precompiled executables for Mac OS X (You may need install GSL to run it. GSL is available from the fink project).
hdhot.pl: a Perl script that processes the output from Hudson's ms program to produce haplotype samples with a recombination hotspot. (Code).

Scripts

run_linkmap.sh (code) and linkpre.pl (code): a pair of scripts to run the linkmap program in LINKAGE for all intervals.

High Performance Statistical Computing

R Packages

rpvm

R interface to PVM (Parallel Virtual Machine), source package available at CRAN. Unix only.

R interface to SPRNG (Scalable Parallel Random Number Generators) library, source package available at CRAN. Here is a Win32 binary version rsprng.zip (186 KB, SIG) . It was statically linked with SPRNG (v2.0a) and GMP (v4.0) libraries. (Notes on Installation)

If you plan to compile rsprng under win32, you will need SPRNG win32 static library sprng2.0a-mingw32.zip (91 KB, SIG) and Gnu MP library. It was surprisingly hard to find precopmpiled libgmp for win32 so I made a static library libgmp-mingw32-static.tar.bz2 (622 KB, SIG) and the latest source can be found here.

Other SPRNG binaries:

sprng-2.0a-i386-darwin.tar.bz2 (108 KB, SIG) (compiled on Intel Mac, Mac OS X 10.4.9 using gcc 4.0.1).
sprng-2.0a-x86_64-linux.tar.bz2 (103 KB, SIG) (compiled under Fedora Core 4 using gcc 4.0.2, with flags -O2 -m64, AMD Operton).
sprng-2.0a-i386-linux.tar.bz2 (99 KB, SIG) (compiled under Redhat 8.0 using gcc 3.2).
sprng-2.0a-ppc-darwin.tar.bz2 (113 KB, SIG) (compiled under Mac OS X 10.2.8 using gcc 3.1. The easiest way to install gmp is through either Fink or DarwinPorts).
sprng-2.0a-alpha-tru64.tar.bz2 (120 KB, SIG)
sprng-2.0a-sparc-solaris.tar.bz2 (103 KB, SIG)