An Alphabetic List |
Genetic Analysis Software
PAGE 1 (A-F)
searchable database: http://www.animalgenome.org/soft/ (NEW!)
March 16, 2012
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.
In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out.
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,
close to 480 programs by November 2008,
and 520 programs by August 2010.
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.
More and more packages are now written in R. To be consistent, I rename any R package in CRAN from [package-name] to R/[package-name]. If a R package is not submitted to CRAN, I will keep its original name. Here is another partial list of statistical genetics R packages summarized by CRAN (http://cran.r-project.org/web/views/Genetics.html). Yet more R packages can be found in: http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/r-genetics.htm, http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm, http://wpicr.wpic.pitt.edu/WPICCompGen/software.htm, http://www-gene.cimr.cam.ac.uk/clayton/software/, among other places.
If you have new programs to add or any updated information, please send a message to firstname.lastname@example.org
what's new |
link to other sources |
page 1 (A-F) | page 2 (G-L) | page 3 (M-P) | page 4 (Q-Z)
a b c d e f | g h i j k l | m n o p | q r s t u v w [x] [y] z
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.
CJ Hoggart, MD Shriver, RA Kittles, DG Clayton, PM McKeigue (2004), "Design and analysis of admixture mapping studies", American Journal of Human Genetics, 74(5):965-978. [html]
CJ Hoggart, EJ Parra, MD Shriver, C Bonilla, RA Kittles, DC Clayton, PM McKeigue (2003), "Control of confounding of genetic associations in stratified populations", American Journal of Human Genetics, 72(6):1492-1504. [html]
PM McKeigue, J Carpenter, EJ Parra, MD Shriver (2000), "Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations", Annals of Human Genetics, 64:171-186.
Gudbjartsson, Jonasson, Frigge, Kong (2000) "Allegro, a new computer program for multipoint linkage analysis", Nature Genetics, 25:12-13.
Gudbjartsson, Thorvaldsson, Gunnarsson, Kong, Ingolfsdottir (2004), "Decision diagram based multipoint linkage analysis: ALLEGRO2", American Journal of Human Genetics, 75(suppl):?.
Gudbjartsson, Thorvaldsson, Kong, Gunnarsson, Ingolfsdottir (2005), "Allegro version 2", Nature Genetics, 37:1015-1016. [PLEASE CITE THIS REFERENCE WHEN USING THE ALLEGRO2 PROGRAM]
Hauser, Watanabe, Duren, Bass, Langefeld, Boehnke (2004), "Ordered subset analysis in genetic linkage mapping of complex traits", Genetic Epidemiology, 27:53-63.
Chung, Hauser, martin (2006), "The APL test: extension to general nuclear families and haplotypes and examination of its robustness", Human Heredity, 61:189-199.
Schneider, Kueffer, Roessli, Excofier, "Arlequin: A software for population genetic data analysis. Ver 1.1", (Genetics and Biometry Lab, Dept. of Anthropology, University of Geneva, 1997);
User's manual (PDF, v1.1)
User's manual (PDF, v3.1)
online manual (PDF)
Beaumont, Balding (2004), "Identifying adaptive genetic divergence among populations from genome scans", Molecular Ecology, 13:969-980.
* phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
* infer sporadic missing genotype data.
* impute ungenotyped markers that have been genotyped in a reference panel.
* perform single marker and haplotypic association analysis.
* detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals.
Browning BR and Browning SR (2007), "Efficient multilocus association testing for whole genome association studies using localized haplotype clustering", Genetic Epidemiology, 31:365-375.
Lu, Niu, Liu (2003), "Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms", Genome Research, 13:2112-2117.
or a copy from http://hpcio.cit.nih.gov/lserver/BLOCK.html
Givry, Bouchez, Chabrier, Milan, Schiex (2005), "CARTHAGENE: multipopulation integrated genetic and radiation hybrid mapping", Bioinformatics, 21(8):1703-1704.
v.1.6 highlights: 1. complete secondary analysis software package, including facilities for alignment, reference-guided assembly, SNP/indel calling and counting for RNA applications. 2. new methods for gapped, multiseed alignments that reduce artifactual mismatches. 3. new indel detection method, and improved SNP calling on longer Genome Analyzer reads.
Buhler, et. al. (1997) Human Heredity, 47(4):211-222.
Satten, Epstein (2004), "Comparison of prospective and retrospective methods for haplotype inference in case-control studies", Genetic Epidemiology, 27(3):192-201
Sun, Levin, Boerwinkle, Robertson, Kardia (2006), "A scan statistic for identifying chromosomal patterns of SNP association", Genetic Epidemiology, 30(7):627-635.
http download: https://sourceforge.net/project/showfiles.php?group_id=27707
Devlin, Jones, Bacanu, Roeder (2002), "Reply to Olson", Genetic Epidemiology, 23(4):449-455.
documentation (version 2.4, 1990).
Tutorial (from biobase.dk)
Yahoo discussion group: http://groups.yahoo.com/group/dchip/
Hoffmann, Lindner (2005), "easyLINKAGE-Plus - automated linkage analyses using large-scale SNP data" Bioinformatics, 21(17):3565-3567.
based on some earlier prototype routines by Jochen Kumm.
Gu, Rao (1997), "A linkage strategy for detection of human quantitative-trait loci: I. Generalized relative risk ratios and power of sib pairs with extreme trait values",. American Journal of Human Genetics, 61(1):200-210. [abstract]
Gu, Rao (1997), "A linkage strategy for detection of human quantitative-trait loci: II. Optimization of study designs based on extreme sib pairs and generalized relative risk ratios", American Journal of Human Genetics, 61(1):211-222. [abstract]
online user's guide
a product review from: http://www.scienceboard.net/resources/prodreviews.asp?cat=22&product=440
Becker, Knapp (2004), "A powerful strategy to account for multiple testing in the context of haplotype analysis", American Journal of Human Genetics, 75:561-570. [html]
Becker, Knapp (2005), "Impact of missing genotype data on Monte-carlo simulation based haplotype analysis", Human Heredity, 59:185-189.
Becker, Cichon, Jönson, Knapp (2005), "Multiple testing in the context of haplotype analysis revisited: application to case-control data", Annals of Human Genetics, 69:1-10
Becker, Schumacher, Cichon, Baur, Knapp (2005), "Haplotype interaction analysis of unlinked regions", Genetic Epidemiology, 29:313-322.
Becker, Valentonyte, Croucher, Strauch, Schreiber, Hampe, Knapp (2006), "Identification of probable genotyping errors by consideration of haplotypes", European Journal of Human Genetics, 14:450-8.
Becker, Baur, Knapp (2006), "Detection of parent-of-origin effects using haplotype analysis", Human Heredity, 62:64-76
S Gerber, P Chabrier, A Kremer (2003), "FaMoz: a software for parentage analysis using dominant, codominant and uniparentally inherited markers", Molecular Ecology Notes, 3(3):479-481.
collarorators for version 4: Ann Becker, Dan Geiger.
ftp://ftp.ncbi.nlm.nih.gov/pub/fastlink (since Aug 6, 1996) or ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/FASTLINK/fastlink
Schaffer, Gupta, Shriram, Cottingham (1994), "Avoiding recomputation in linkage analysis", Human Heredity, 44:225-237. ( PDF)
online README files (version 3.0P, december 95).
Dwarkadas, Schaffer, Cottingham, Cox, Keleher, Zwaenepoel, "Parallelization of general linkage analysis problems", ( PDF)
Gupta, Schaffer, Cox,Zwaenepoel, "Integrating parallelization strategies for linkage analysis", ( PDF)
Schaffer, "Faster linkage analysis computations for pedigrees with loops or unused alleles", ( PDF)
Becker, Geiger, Schaffer, "Automatic selection of loop breakers for genetic linkage analysis", Human Heredity, ( PDF)
Becker, Bar-Yehuda, Geiger, "Random algorithms for the loop cutset problem", ( PDF)
Schaffer, "Loops in FASTLINK", ( PDF)
Schaffer, "The mystery of (the) unknown", ( PDF)
Schaffer, "Pedigree traversal in FASTLINK", ( PDF)
registration page at: http://watson.hgen.pitt.edu/register
online manual pages (same as slink)
Laird, Horvath, Xu (2000), Implementing a unified approach to family based tests of association, Genetic Epi, supp 1, 19:36-42; Rabinowitz, Laird (2000), A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information, Human Heredity, 50:211-223.
Horvath, Xu, Laird (2001), The family based association test method: strategies for studying general genotype-phenotype associations, European J Hum Genet. 9:301-306.