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: April 21, 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, and close to 400 programs by December 2006. 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.
de Andreade, Amos, Thiel (1999), "Methods to estimate genetic parameters for quantitative traits", Genetic Epidemiology, 17(1):64-76.