linkage software list (obsolete)

An Alphabetic List
of
Genetic Analysis Software
OBSOLETE

Un-maintained, Web-less programs

B-TEST

full name:
version:
descriptions:
authors: Neil Risch (Stanford University)
web:
ftp:
source code language: FORTRAN
operating systems:
executables:
reference: Risch, Am J. Hum Genet, 42, 353-364 (1988)

C-GEN

full name:
version:
descriptions: "c-test" ("c" may refer to "combination" of two used procedures, or simply to the next test introduced after Risch's "b-test") of locus heterogeneity
authors: C. J. MacLean (Medical College of Virginia)
web:
ftp:
source code language:
operating systems:
executables:
reference: MacLean,Ploughman, Diehl, Kendler, Am J. Hum Genet, 50, 1259-1266 (1992)

CHRSIM

full name: CHRomosome-base SIMulation

version:

descriptions:

authors: Marcy Speer ( marcy@genemap.mc.duke.edu), Joe Terwilliger, Jurg Ott (Columbia Univ)
web:
ftp: .
source code language: Pascal
operating systems:
executables:
reference: Am Soc Hum Genet annual meeting 1992 (Speer, Terwilliger, Ott, Am J Hum Genet, 51 Supp,A202 (1992));
Terwilliger,Speer, Ott, Genetic Epid. 10, 217-224 (1993)

CINTMAX

full name:

version:

descriptions: a modified version of CILINK (of LINKAGE package) which is capable of analyzing CEPH pedigree data under a variaty of possible models of interference.

authors: Daniel E. Weeks (Univ of Oxford and Univ of Pittsburg, dweeks@watson.hgen.pitt.edu )
web:
ftp: ftp://watson.hgen.pitt.edu/pub
source code language: Pascal
operating systems:
executables: cintmax
reference: Am Soc Hum Genet annual meeting 1991 (Weeks,Ott, Lathrop, Am J. Hum Genet,Supp, 49,372 (1991))

CPROP

full name: Constraint PROPagator

version:

descriptions: rule-based program for constructing genetic maps

authors: Stanley Letovsky, ( letovsky@gdb.org ) M. Berlyn
web:
ftp:
source code language:
operating systems:
executables:
reference: Letovsky, Berlyn, Genomics, 12, 435-446 (1992)

DBLINK

full name: Data Base management system for LINKage analysis

version: 2.18 (June 1995)

descriptions: A complete "dBASE IV" format database system, including a full dBASE utility routine. Import/export and file conversion facilities. Creates and converts files for (and/or between) LINKAGE, LIPED, HOMOG, SEXLODS, CRIMAP and CEPH. Produces informative outputs and summary tables from all of the LINKAGE modules.

authors: Mansoor Sarfarazi (Univ Connecticut Health Center, msarfara@cortex.uchc.edu )
web: http://cortex.uchc.edu/~msarfara/
ftp:
source code language: Clipper / dBASE IV
operating systems: PC(DOS)
executables: dBlink.EXE
reference: Am Soc Hum Genet annual meeting 1990 (Sarfarazi, Am. J. Hum. Genet. suppl. 47, A198 (1990)).
Sarfarazi, Clinical Genetics, 40(2), 105 (1991).

DISEQ

full name:

version 1.2 (feb 22, 1996)

descriptions: a likelihood-based approach to test linkage disequilibrium for multiple loci

authors: Joe Terwilliger ( joe@linkage.cpmc.columbia.edu )
web: see a mirror at: http://www.hgmp.mrc.ac.uk/Registered/Option/diseq.html
ftp: ftp://ftp.well.ox.ac.uk/pub/genetic/diseq or ftp://linkage.cpmc.columbia.edu/software/diseq
source code language: Pascal
operating systems: UNIX (OSF1/SunOS/..), VMS
executables: dislamb, dismult,tdtlike,mcnlike
reference: Terwilliger, Am J Hum Genet, 56, 777-787 (1995).
online documentations (feb 1996 version)

DMAP (1)

full name: Disequilibrium MAP

version:

descriptions: a composite likelihood model is used to take into account the information from all disease_locus-marker pairs while modeling the variability in the disequilibrium values due to the evolutionary dynamics of the population

Authors: Bernie Devlin (email: devlinbj@msx.upmc.edu)
web: http://wpicr.wpic.pitt.edu/wpiccompgen/
ftp:
source code language: FORTRAN
operating systems:
executables:
reference: Devlin, Risch, Roeder, "Disequilibrium mapping: composite likelihood for pairwise disequilibrium", Genomics, 36(1), 1-16 (1996).

DMS

full name: Database Management System (For use with Positional Mapping Projects)

version: Last Version April 1997

descriptions: A complete "dBASE IV" format database system.

Authors: Mansoor Sarfarazi (University of Connecticut Health Center; email: msarfara@cortex.uchc.edu )
web/ftp: http://cortex.uchc.edu/~msarfara/ (not available)
source code language: Clipper / dBASE IV
operating systems: MS-DOS
executables: dms.exe
reference: a brief description

ESPA

full name: Extended Sib Pair Analysis

version:

descriptions:

authors: Lodewijk Sandkuijl ( sandkuyl@rullf2.leidenuniv.nl)
web:
ftp:
source code language: FoxBase
operating systems: PC(DOS/..)
executables:
reference: Sandkuyl in "Multipoint Mapping and Linkage Based Upon Affected Pedigree Members: Genetic Analysis Workshop 6" eds. Elston, Spence, Hodge, MacCluer (Alan R. Liss, 1989)

EXCLUDE

full name:
version:
descriptions: exclusion mapping
authors: John Edwards
web:
ftp:
source code language: Pascal
operating systems: PC(DOS/..)
executables:
reference: Edwards, J. Med Genet, 24, 539-543 (1987)

GCONVERT (see SIB-PAIR instead)

GENETREE

full name: GeneTree

version: 1.0

descriptions: Pedigree drawing software for PCs and compatibles. Does not require Windows. Designed to work as an add-on to any database which can produce ascii files.

authors: Robert Hodges. contact: Ellen Wijsman (Univ Washington, wijsman@max.u.washington.edu )
web: [not in public domain]
ftp: [not in public domain]
source code language: C
operating systems: PC(DOS/..)
executables: genetree.exe, sc.exe
reference:
price: US$125

GENO

full name:

version:

descriptions: genotype data entering program (the output can be used directly for LINKAGE package, or merge directly into CEPH database)

authors: Matt Stephenson ( stephenm@webchlc.mfldclin.edu)
web:
ftp: ftp://dgabby.mfldclin.edu/pub/geno
source code language:
operating systems: PC (DOS/Window 3.1.1/Window NT)
executables:
reference:

GENODB

full name: GENOtype DataBase

version: 1.0 (beta version)

descriptions: A Microsoft Access database management system to manipulate large amounts of genotype data generated with fluorescently labeled dinucleotide markers.

Authors: Jin-Long Li (jllee@creighton.edu), Hong-Wen Deng (deng@creighton.edu)
web/ftp: http://osteoporosis.creighton.edu (coming soon)
source code language: Visual Basic, Embedded SQL
operating systems: MS-Windows (NT/2000...) with Microsoft Access installed
executables:
reference: Li et al, Genome Research, 11(7):1304-1314 (2001).

GSCAN

full name: Genomic Software for Complex Analysis of Nucleotides

version: 1.0 (Oct, 1998)

descriptions: Allows semiparametric two-point linkage, linkage-disequilibrium, and combined linkage/linkage-disequilibrium analysis of general pedigree data for discrete traits from an internet browser, including: pedigree consistency checks and pedigree drawing, gene-gene and gene-environment interaction incorporation, Z-score computation, and e-mailed final results.

authors: Lue Ping Zhao ( lzhao@fhcrc.org), Fil Quiaoit ( filq@fhcrc.org), Corinne Aragaki ( caragaki@fhcrc.org), Li Hsu ( lih@fhcrc.org) (Fred Hutchinson Cancer Research Center)
web/ftp: http://cougar.fhcrc.org/~filq/html/main.htm
source code language: C++,Java
operating systems: WWW
executables:
reference: Zhao, Quiaoit, Hsu, Aragaki(1998), American Journal of Medical Genetics, 77:366-383; Zhao, Quiaoit, Aragaki, Hsu (1998), American Journal of Medical Genetics, 79:48-61; Zhao, Aragaki, Hsu, Quiaoit (1998), American Journal of Human Genetics, 63:225-240; Zhao, Quiaoit, Aragaki, Hsu, submitted.

KINDRED

full name:

version: 1.0

descriptions: a program that 1. Stores and maintains data on families and members of families, and 2. Automatically draws pedigrees in a format suitable for presentation/publication.

authors: "Epicenter Software" (p.o.box 90073, Pasadena, CA 91109. tel: 818-304-9487; FAX: 818-449-0437): Jonathan Buckley (Dept of Preventive Medicine, USC, jbuckley@hsc.usc.edu)
web/ftp: http://icarus2.hsc.usc.edu/epicenter/kindred.html
source code language:
operating systems: MS-DOS, MS-Windows (95/NT)
executables:
reference:
price: US$475 for single user license

LABMAN/LINKMAN

full name: Laboratory Management /Linkage analysis and lod score data Management

version: 2.0 (May 1996)

descriptions:

authors: Phillip Adams (New York State Psychiatric Institute, pa1@columbia.edu )
web:
ftp: ftp://ftpchild.cpmc.columbia.edu/sys/share/labman20
source code language: FoxPro
operating systems: PC(DOS/..)
executables:
reference: P Adams (1994), "LABMAN and LINKMAN: a data management system specifically designed for genome searches of complex diseases", Genetic Epidemiology, 11(1):87-98.

linkage utility programs

full name:

version:

descriptions:

authors: Jurg Ott (Rockefeller University)

web/ftp: http://www.genemapping.cn/LinkUtil.zip
source code language: Pascal
operating systems: MS-Windows
executables: 2by2, associate, binom, chiprob, counting, crossover, equiv, hhwe, hist, mapfun, norinv, norprob, permute, het, reri, sexdif, varco3, varco6
reference: online documentation at http://www.genemapping.cn/linkutil.htm

LIPIN

full name:
version:
descriptions: data entry and management program for LIPED
authors: James Trofatter (Massachusetts General Hospital)
web:
ftp:
source code language: Pascal
operating systems: PC(DOS/..)
executables:
reference: Trofatter, Haines, Conneally, Am J. Hum Genet, 39, 147-148 (1986)

LOOPS [it is now part of "makeped"]

full name:

version:

descriptions:

authors: Xiaoli Xie, Jurg Ott

web:

ftp:

source code language: Pascal

operating systems: PC(DOS/..)

executables:

reference: Am Soc Hum Genet annual meeting 1992 (Xie, Ott, Am J Hum Genet, suppl, 51, A206).
see also: loops in fastlink .

MAP MANAGER CLASSIC

full name:

version : 2.6.6 (April 2, 1999)

descriptions: A graphic, interactive program to map Mendelian loci using intercrosses with codominant markers, backcrosses or recombinant inbred strains in experimental plants or animals.

authors: K.F. Manly

web/ftp: http://www.mapmanager.org/mapmgr.html
source code language: Pascal
operating systems: MacOS
executables:
reference: Manly, Mammalian Genome, 4:303-313 (1993)

MDMAP

full name: Minimum Distance Map

version:

descriptions:

authors: Cathy Falk (email: cathy@server.nybc.org )
web:
ftp:
source code language: FORTRAN
operating systems: UNIX, PC (DOS/..)
executables:
reference: Falk, Genomics, 9, 120-123 (1991)

MOM

full name: Maximized-Over-Model
version:
descriptions:
authors: Jurg Ott, Joe Terwilliger (Columbia Univ)
web:
ftp:
source code language: Pascal
operating systems: VMS
executables:
reference: Terwilliger, Ott, Cytogenetics and Cell Genet. 59, 142-144 (1992)

PEDI

full name:

version:

descriptions: using incremental programming technique to calculate pedigree likelihood that is more efficient than CMAP.

authors: Robert Karmer, Daniel Weeks (email: dweeks@watson.hgen.pitt.edu ), Donald Chiarulli
web:
ftp: watson.hgen.pitt.edu (not available yet)
source code language: C
operating systems: UNIX
executables:
reference: Kramer, Weeks, Chiarulli, Hum. Hered. 45, 323-336 (1995 )

PEDSCORE

full name:
version:
descriptions: Morte Carlo methods and Identical by Descent statistics to test deviation from Mendelian expectation.
authors:
web:
ftp:
source code language:
operating systems:
executables:
reference: Weitkamp, Lewis, Cytogenet Cell. Genet. 51, 1105-1106 (1989)

PGR

full name: Parental Genotype Reconstruction

version:

descriptions:

Authors: Rory Martin (email: rmartin@bara.psi.vcu.edu)
web/ftp: http://electro.psi.vcu.edu:80/~rmartin/software/pgr_software.html
source code language: FORTRAN
operating systems: UNIX
executables:
reference: Martin, Alda, MacLean (1998), Genetic Epidemiology, 15:471-490.

PLOT2000

full name:
version:
descriptions:
authors: G. Wolak, M. Sarfarazi
web:
ftp:
source code language: dBASE
operating systems:
executables:
reference: Clinical Genetics Soc meeting (1986) (Wolak, Sarfarazi, J. Med Genet, 24,246-247 (1987)

REGRESS

full name:
version:
descriptions: regression models for segregation analysis are extended to include multivariate data and linked marker loci.
authors: George Bonney
web:
ftp:
source code language:
operating systems:
executables:
reference: Bonney, Lathrop, Lalouel, Am J Hum Genet, 43, 29-37 (1988)

SCHESIS

full name:
version:
descriptions: pedigree drawing and error checking for the input data
authors: Anthony Round
web:
ftp:
source code language:
operating systems:
executables:
reference: Am Soc Hum Genet annual meeting 1990 (Round, Am J. Hum Genet, suppl 46, A75 (1990))

SENSEN/SENPED

full name: Sensitivity Analysis

version:

descriptions: analyze the effect on lod score when one individual in the data set changes diagnostic or recombination states

authors: Susan Hodge (Columbia Univ), David Greenberg (Mt Sinai School of Medicine, miriam@onion.salad.mssm.edu )
web:
ftp:
source code language: Pascal
operating systems:
executables:
reference: Hodge, Greenberg, Am J. Hum Genet, 50, 1053-1066 (1992)

SIGMA

full name: System for Integrated Genome Map Assembly

version:

descriptions:

authors: Michael Cinkosky, Jim Fickett, Michael Bridgers, William Barber, Mohamad Ijadi, Charles Troup

web: http://www.ncgr.org/sigma/home.html
ftp:
source code language: C++, X/Motif, ObjectStone
operating systems: UNIX(SunOS/OSF1/..),MacOS
executables:
reference:

URP

full name:
version:
descriptions:
authors: Michael Braverman
web/ftp:
source code language: PL/I, Pascal
operating systems:
executables:
reference: Braverman, Computer and Biomed Res, 18, 24-36 (1985)

genetic analysis software list: www.nslij-genetics.org/ga/soft (obsolete)