galaxy1

galaxy1 GENETIC LINKAGE ANALYSIS PROGRAMS

AVAILABLE TO NIH RESEARCHERS

ON CIT HIGH-PERFORMANCE COMPUTER SYSTEMS

Please see the galaxy and spica systems home pages for information about these high-performance multi-CPU computers and creating an account to use these programs. You will need to have a helix account before you can get an account on galaxy or spica. There is a small monthly charge to have a helix account, but galaxy and spica accounts are at no extra charge.

Please contact Ed Suh (suh@helix.nih.gov) for more information about gaining access to these programs.

Galaxy is a Silicon Graphics Origin 2000 system with thirty-two R10000 CPUs. Spica is an IBM SP2 parallel computer with one hundred four RS/6000 CPUs.

No.	Name	Date	Authors/Affiliation	Executable	Galaxy¹	Spica²	Remarks / Description
1	ACT ver. 1.0	06/1997	Christopher Amos, Mariza de Andrade, Dakai Zhu, Liping Yu	ibd ml ql he ibdn multic	Yes Yes Yes Yes Yes Yes	No No No No No No	This software currently contains an 'ibd' program that calculates the proportion of genes identical by descent for a nuclear family, 'ml' which uses maximum likelihood methods to provide estimates of variance components for quantitative traits using linked markers, 'ql' which estimates variance components using quasilikelihood methods (for not so normally distributed data), 'multic' which performs maximum likelihood analysis for multivariate data with or without ascertainment corrections, and 'ibdn' which is a modification of the ERPA program to provide i.b.d. calculations for extended pedigrees and to be used with ml, ql, or multic.
2	APM	1993	Dan Weeks (U. of Pittsburg), Mark Schroeder	apm sim apmmult simmult chapm hist	No Yes No Yes Yes Yes	No No No No No No	'No' on Galaxy because it is written in Pascal. This program is designed to efficiently compute the APM statistic for a number of pedigrees over a number of marker loci. It is capable of storing the results of kinship calculations internally, greatly speeding up computations for different markers on the same pedigree. It can also store kinship information in a file to be used later.
3	ASPEX ver. 2.0	11/1998	David Hinds (Stanford U.), Neil Risch (Stanford U.)	sib_ibd sib_tdt sib_phase sib_map	Yes Yes Yes Yes	No No No No	A set of programs for performing multipoint exclusion mapping of affected sibling pair data for discrete traits.
4	BETA	01/1998	Collins, NE Morton	beta	Yes	No	Non-parametric linkage analysis using allele sharing in sib pairs
5	CASPAR	1997	Richa Agarwala (NIH/NCBI), Alejandro Schäffer (NIH/NCBI)	caspar	Yes	No	CASPAR's main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing.
6	CRI-MAP ver. 2.4	03/1990	Phil Green (U. Of Washington)	crimap	Yes	No	Constructing multilocus linkage map
7	CRI-MAP-PVM	1990	Tara Matise, Mark Schroeder, Donald Chiarulli, Dan Weeks		Not Yet	No	PVM available in Galaxy soon. A parallel version of CRI-MAP
8	FASTLINK ver. 4.0P	10/1997	Alejandro Schäffer (NIH/NCBI), Cottingham, Gupta, Idury, Shriram	Ilink mlink linkmap lodscore unknown	Yes Yes Yes Yes Yes	Yes Yes Yes Yes Yes	FASTLINK is a software package to do the computations for genetic linkage analysis. Genetic linkage analysis is a statistical technique used to map genes and find the approximate location of disease genes.
9	GASSOC ver. 1.01	01/1997	D.J. Schaid, C. M. Rowland, (Mayo Clinic / Foundation)	gassoc	Yes	No	Statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the suhsmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms.
10	GASP ver. 3.3	10/1997	A. F. Wilson (NIH/NHGRI), J. E. Bailey-Wilson, E. W. Pugh, A. J. M. Sorant (NIH/NHGRI)	gasp_v33.o prng_v33.o	Yes	No	User provides driver code to run GASP. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models.
11	GeneHunter ver. 2.0 beta	11/1998	Leonid Kruglyak, Mark Daly, Mary Reeve-Daly, Eric Lander (Whitehead Institue	gh	Yes	No	Multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction
12	GeneHunter-Plus ver. 1.1	10/1997	Augustine Kong, Mike Friggs	ghp	Yes	No	GENEHUNTER-PLUS is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively).
13	PGeneHunter-Plus ver. 1.1			ghp	Test	Test	Parallel version is under development
14	HARDY ver.07/96	07/1996	Sun-Wei Guo(U. of Minnesota), E.A. Thompson (U. Washington)	hwe	Yes	No	Markov chain Monte Carlo program for association in two-dimensional contingency tables, and for testing Hardy-Weinberg equilibrium.
15	Linkage Auxiliary Programs		Peter Cartwright (U. Utah)	lcp lsp lrp makeped preplink	Yes Yes Yes Yes Yes	No No No No No
16	MapMaker/HOMOZ ver. 05/95	05/1995	Leonid Kruglyak, Mark Daly, Eric Lander (Whitehead Inst.)	homoz	Yes	No	Calculates multipoint lod scores in pedigrees with inbreeding loops.
17	MapMaker/SIBS ver. 2.1	12/1996	Leonid Kruglyak, Mark Daly, Eric Lander (Whitehead Inst.)	sibs	Yes	No
18	MLBGH ver. 1.0		Lauren Abel (France), Muller-Myhsok (Germany), Anne Philippi (France)	mlbgh	Yes	No	An extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method.
19	Sage ver. 4.0 beta	12/1998	R. Elston, J. Bailey-Wilson, G. Bonney, L. Tran, Keats, A. Wilson. (Dept. of Epedemiology and Biostatistics, Rammelkamp Center for Education and Research Metrohealth Campus)	gen_ibd genibd mlod pedinfo sibpal2	Yes Yes Yes Yes Yes	No No No No No	The S.A.G.E. software provides researchers with the tools necessary for various types of statistical genetic analysis of human family data.
20	Sib-Pair ver. 0.94.6	1997	David Duffy (Australia)	sib-pair	Yes	No	A program for simple non-parametric genetic analysis. Includes IBD and IBS based APM, Haseman-Elston sib pair, TDT and association analyses.
21	SimCross ver. 06/95	06/1995	Dan Weeks (U. of Pittsburg)	simcross	Yes	No	programs for generating optimal haplotype configurations on general pedigrees using a likelihood-based approach to correctly take intermarker recombination fractions into account. simcross ignores untyped parts of the pedigree, and it uses simulated annealing
22	SimIBD ver. 2.1	01/1998	Dan Weeks, Sean Davis (U. of Pittsburg)	simibd	Yes	No	SIMIBD calculates a linkage statistic in general pedigrees based on marker allele sharing among all affected individuals.
23	PSimIBD ver. 2.1	09/1998	Dan Weeks, Sean Davis, Ed Suh (CIT/NIH), Ed Suh	simibd	Yes	Yes	Parallel version of SimIBD
24	Slink ver. 2.5	08/1998	Dan Weeks, Jurg Ott	slink	Yes	No	SLINK takes a sample of pedigrees segrating a disease or trait as input. Under an assumed genetic model for the trait locus, the program simulates replicates of the input pedigree sample where genotypes at a markers locus linked to the trait locus (recombination fraction and marker allele frequencies specified by the user) have been simulated.
25	Pslink ver. 2.4	02/1998	Dan Weeks, Jurg Ott, Ed Suh (CIT/NIH), Ed Suh	slink	Yes	Yes	Parallel version of Slink
26	PedCheck ver. 1.1	11/1998	J. R. O'Connell	pedcheck_sgi	Yes	No	Identify all Mendelian inconsistencies in pedigree data.
27	Vitesse ver. 2.0	07/1998	Jeff O'Connell	vitesse	Yes	No	Calculates likelihood on pedigrees.

Note:

Galaxy is a SGI Origin2000 parallel computer system. All executable files are in the '/local/bin' directory, and all documents are in the '/usr/local/doc'.
Spica is an IBM SP2 parallel computer system. PSLINK executable file is in the '/system/dest/rs_aix41/slink/bin/', and the documents are in the '/system/dest/rs_aix41/slink/doc/slink/'. PSimIBD executable file is in the '/system/dest/rs_aix41/simibd/bin/', and the documents are in the '/system/dest/rs_aix41/simibd/doc/simibd/'.