Rosenberg lab at Stanford University


haploconfig is a program that can be used to implement tests of neutrality based on the frequency distribution of haplotypes in a sample of DNA sequences (the "haplotype configuration") and the number of segregating sites. The neutrality tests can be performed conditional on the standard neutral coalescent model with or without recombination, exponential population growth, or island migration. A description of the method underlying the program can be found in "Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites" Genetics 169: 1763-1777 (2005). The haploconfig program can also be used as a coalescent simulator for models with or without recombination.

The software is for Windows or Linux. Executables for both systems are included in the download.

[Download software package (includes the manual)] (you will be directed first to a registration page and we would very much appreciate if you register)
[Download manual]
[Download article Genetics 169: 1763-1777 (2005)]

Winzip will unzip the Windows version. To use the program in linux, unzip and untar the files in an appropriate directory using

gunzip haploconfig.tar.gz; tar xvf haploconfig.tar

Please send comments or problems with haploconfig to Noah Rosenberg.

Software history

July 31, 2007 - upload of version 1.1
March 31, 2005 - initial upload of manual and software