linkage software list (page 1)

An Alphabetic List
of
Genetic Analysis Software
PAGE 1 (A-F)

URL
master: http://www.nslij-genetics.org/soft/
mirror: http://linkage.rockefeller.edu/soft/
searchable database: http://www.animalgenome.org/soft/ (NEW!)

Last Update: September 05, 2008

Computer software on the following topics are included here: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. This list is offered here as a service to the gene mapping community. The inclusion of a program should not be interpreted as an endorsement to that program from us.

This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 460 programs by June 2008. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School.
Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.
If you have new programs to add or any updated information, please send a message to webadm@nslij-genetics.org

ACT

full name: Analysis of Complex Traits

version: 1.1 (Mar 17,2000)

descriptions: It contains the following modules: ibd, calculates the proportion of gene shared identical by decent for a nuclear family; ibdn, (modified program of ERPA), which implements a method for assessing increased-allele sharing between all pairs of affected relatives within a pedigree; multic, multivariate analysis for complex traits; ml, estimation of variance components using maximum likelihood; ql, estimation of variance components using quasi likelihood; relcov, generates first degree relationship coefficients for extended families; sim2s, the simulation program that was used to test ACT; cage, Cohort Analysis for Genetic Epidemiology; gh: GeneHunter, heavily modified to assist multipoint calculation using multic; TDT: TDT programs written in SAS gcc and f77 compilers are necessary. Executable programs are included for compatible operating system, i.e., Solaris2.6.

authors: Christopher I. Amos (email: camos@request.mdacc.tmc.edu ), Mariza de Andrade (email: mandrade@request.mdacc.tmc.edu ), JianFang Chen (email: cjf@request.mdacc.tmc.edu)
web/ftp: http://www.epigenetic.org/Linkage/act.html
http://www.epigenetic.org/Linkage/act.tar.gz
source code language: Fortran77,C++
operating systems: UNIX(Solaris 2.4/..)
executables: ibd, ml, ql, he, ibdn, multic
reference: Amos, et al (1996), "Assessing genetic linkage and association with robust components of variance approaches", Annals of Human Genetics, 60:143-160.
Amos (1994), "Robust variance-components approach for assessing genetic linkage in pedigrees", American Journal of Human Genetics, 54:535-543. [abstract]
de Andreade, Amos, Thiel (1999), "Methods to estimate genetic parameters for quantitative traits", Genetic Epidemiology, 17(1):64-76.