Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00109 NAME FASTLINK DOMAIN Genetic Linkage software DESCRIPTION Faster Sequential Genetic Linkage Computations DESCRIPTION modified versions of the general pedigree programs of LINKAGE 5.1 AUTHOR Robert Cottingham, Ramana Idury, Alejandro Schaffer, K. Shriram, AUTHOR and Sandeep Gupta. RA Cottingham R.W., Idury R.M., Schaffer A.A.; RT "Faster Sequential Genetic Linkage Computations."; RL Am. J. Hum. Genet. 53: 252-63(1993). RX Medline; 93304419. ADDRESS Department of Cell Biology, Baylor College of Medicine, ADDRESS Houston, TX 77030, USA. CONTACT schaffer@cs.rice.edu SITE ftp anonymous softlib.cs.rice.edu SITE Directory /pub/linkage SITE-CONTACT schaffer@cs.rice.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/FASTLINK SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C VOLUME - AC BC00110 NAME Linkage Analysis Package DOMAIN Genetic Linkage software DESCRIPTION The Linkage Analysis Package (LINKAGE) is an integrated system DESCRIPTION of programs designed to perform linkage analysis and genetic DESCRIPTION risk calculations. AUTHOR Lathrop GM, Lalouel JM RA Lathrop G.M., Lalouel J.M., Julier C., Ott J.; RT "Strategies for multilocus linkage analysis in humans."; RL Proc. Natl. Acad. Sci. U.S.A 81:3443-3446(1984). RA Lathrop G.M., Lalouel J.M., Julier C., Ott J.; RT "Multilocus linkage analysis in humans: detection of RT linkage and estimation of recombination."; RL Am. J. Hum. Genet. 37:482-498(1985). RA Ott J.; RT "Analysis of Human Genetic Linkage (revised edition)."; RL Johns Hopkins University Press, Baltimore, 1991. RA Terwilliger J.D., Ott J.; RT "Handbook of Human Linkage Analysis."; RL Johns Hopkins University Press, Baltimore, 1994. ADDRESS - CONTACT The original versions of the programs may be obtained from CONTACT Mark.Lathrop@wellcome-genetics.oxford.ac.uk SITE ftp anonymous gc.bcm.tmc.edu SITE Directory /pub/linkage SITE-CONTACT bwc@bcm.tmc.edu SITE gopher Host: corona.med.utah.edu Port: 70 (Unix version) SITE URL gopher://corona.med.utah.edu:70/11/pub/software/linkage SITE-CONTACT paulleo@corona.med.utah.edu OS Sun Unix, Vax/VMS, PC (DOS, OS2), Dec ALPHA (OSF1) LANGUAGE Turbo Pascal 5 , NDP Pascal, Pascal, C VOLUME - AC BC00111 NAME MAPMAKER DOMAIN Genetic Linkage software DESCRIPTION MAPMAKER/EXP is a linkage analysis package designed to help DESCRIPTION construct primary linkage maps of markers segregating in DESCRIPTION experimental crosses. MAPMAKER/EXP performs full multipoint DESCRIPTION linkage analysis (simultaneous estimation of all recombination DESCRIPTION fractions from the primary data) for dominant, recessive, and co- DESCRIPTION dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an DESCRIPTION experimental-cross-only successor to the original MAPMAKER DESCRIPTION program. MAPMAKER/QTL is a companion program to MAPMAKER/EXP DESCRIPTION which allows one to map genes controlling polygenic quantitative DESCRIPTION traits in F2 intercrosses and BC1 backcrosses relative to a DESCRIPTION genetic linkage map. AUTHOR Stephen E. Lincoln, Mark J. Daly, and Eric S. Lander RA Lander E., Green P.; RT "Construction of multilocus genetic maps in humans."; RL Proc. Nat. Acad. Sci. U.S.A 84:2363-2367(1987). RX Medline; 87175673. RA Lander E.S., Green P., Abrahamson J., Barlow A., Daly M.J., RA Lincoln S.E., Newburg L.; RT "MAPMAKER: an interactive computer package for constructing primary RT genetic linkage maps of experimental and natural populations."; RL Genomics 1:174-181(1987). RX Medline; 88085192. RA Lander E.S., Botstein D.; RT "Mapping an factors underlying quantitative traits using RT RFLP linkage maps."; RL Genetics 121:185-199(1989). RX Medline; 89137948. RA Paterson A.H., Lander E.S., Hewitt J.D., Peterson S., Lincoln S.E., RA Tanksley S.D; RT "Resolution of quantitative traits into mendelian factors using a complete RT RFLP linkage map."; RL Nature 335:721-726(1988). RX Medline; 89014741. RT Lincoln S., Lander E.S.; RT "Systematic Detection of Errors in genetic linkage data."; RL Genomics 14:604-610(1992). RX Medline; 93052389. ADDRESS Massachusetts Institute of Technology, Center for Genome ADDRESS Research, and Whitehead Institute for Biomedical Research ADDRESS Nine Cambridge Center, Cambridge, Massachusetts, 02142, USA CONTACT MAPMAKER c/o Dr. Eric Lander Whitehead Institute for Biomedical CONTACT Research 9 Cambridge Center Cambridge, Massachusetts 02142, USA CONTACT Internet: mapmaker@genome.wi.mit.edu SITE ftp anonymous ftp-genome.wi.mit.jedu SITE Directory /distribution/mapmaker3 SITE-CONTACT ert@genome.wi.mit.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mapmaker SITE-CONTACT Don Gilbert: gilbertd@cricket.bio.indiana.edu OS Sun SPARCStations running SunOS 4.x (Sun's Unix) OS will work (with some small code modifications) on many flavors of Unix LANGUAGE - VOLUME - AC BC00112 NAME MULTIMAP DOMAIN Genetic Linkage software DESCRIPTION A Program for Automated Genetic Linkage Mapping DESCRIPTION MultiMap is designed to automate the process of genetic linkage DESCRIPTION mapping by using heuristics for map construction. DESCRIPTION Program for Linkage Analysis : CRI-MAP DESCRIPTION Dr. Phil Green (Washington University, St. Louis) DESCRIPTION distribute a modified version of the CRI-MAP program DESCRIPTION (version2.41m) along with MultiMap. The changes made to DESCRIPTION CRI-MAP for compatibility with MultiMap relate only to the DESCRIPTION format of CRI-MAP output. AUTHOR Tara Cox Matise , Mark Perlin & Aravinda Chakravarti RA Matise T.C., Perlin M., Chakravarti A.; RT "Automated construction of genetic linkage maps using an expert RT system (MultiMap) : a human genome linkage map."; RL Nat. Genet. 6:384-390(1994). RX Medline; 94332147. ADDRESS Tara Matisse (tara@linkage.rockefeller.edu) ADDRESS Lab of Statistical Genetics ADDRESS The Rockefeller University ADDRESS 1230 York Ave, Box 192 New York, NY 10021 - USA ADDRESS FAX : 1-212-327-7996 ADDRESS Aravinda Chakravarti (axc39@po.cwru.ed) ADDRESS Department of Genetics, BRB 721 ADDRESS Case Western Reserve University, 10900 Euclid Avenue ADDRESS Cleveland, OH 44106, USA ADDRESS FAX : 1-216-368-3432 CONTACT tara@linkage.rockefeller.edu SITE ftp anonymous linkage.rockefeller.edu SITE Directory /multimap SITE-CONTACT tara@linkage.rockefeller.edu SITE WWW Server at URL http://linkage.rockefeller.edu/multimap OS Sun - Dec - HP LANGUAGE Common Lisp VOLUME - COMMENT mailing list : send a e-mail to multimap@chimera.gene.cwru.edu COMMENT and ask to be added to the list. AC BC00113 NAME SENSEN and SENPED DOMAIN Genetic Linkage software DESCRIPTION Short Fortran programs designed to facilitate basic sensitivity DESCRIPTION analyses of families, as described in Hodge and Greenberg DESCRIPTION SENSEN takes a standard LIPED input file with data for one family DESCRIPTION and prepares equivalent LIPED input files, reversing the DESCRIPTION affectedness status at the main trait for each family member, one DESCRIPTION at a time. SENPED takes the lod file output of LIPED runs on all DESCRIPTION the sensitivity files for a single family (and a single marker) DESCRIPTION and creates an input file for the Pedigree/Draw program , DESCRIPTION showing the original lod score and the difference in lod score DESCRIPTION caused by each change in affectedness status. AUTHOR David A. Greenberg (dag@shallot.salad.mssm.edu) RA Hodge S.E., Greenberg D.A.; RT "Sensitivity of lod scores to changes in diagnostic status."; RL Am J Hum Genet 50:1053-66(1992). RX Medline; 92238489. ADDRESS Department of Psychiatry, Box 1229, Mt. Sinai Medical Center ADDRESS 1 Gustave Levy Place New York, NY 10029, USA CONTACT miriam@onion.salad.mssm.edu SITE - SITE-CONTACT - OS - LANGUAGE FORTRAN VOLUME - AC BC00437 NAME MIM DOMAIN Genetic Linkage software DOMAIN Genetic and Physical Mapping DOMAIN Statistical significance DOMAIN Multivariate analysis DESCRIPTION MIM is a program to implement the Multipoint IBD method for DESCRIPTION partitioning genetic variance of quantitative traits to DESCRIPTION specific chromosomal regions using data on nuclear families. AUTHOR David E. Goldgar, Cathryn M. Lewis, Khosrow Gholami, AUTHOR Edward N. Kort RA Goldgar D.E.; RT "Multipoint analysis of human quantitative genetic variation."; RL Am. J. Hum. Genet. 45:957-967(1990). RA Goldgar D.E., Oniki R.O.; RT "Comparison of a multipoint identity by descent method with RT parametric multipoint linkage analysis for mapping quantitative traits."; RL Am. J. Hum. Genet. 50:598-606(1992). ADDRESS Cathryn Lewis, Ph.D. ADDRESS Genetic Epidemiology ADDRESS 391 Chipeta Way, D2 ADDRESS Salt Lake City, UT 84108, USA CONTACT edward@episun2.med.utah.edu SITE ftp anonymous morgan.med.utah.edu SITE Directory /pub/Mim SITE-CONTACT - OS UNIX LANGUAGE C VOLUME 250K bytes REQUIRES - COMMENTS Copies of the program may be obtained COMMENTS by contacting Edward Kort at edward@episun2.med.utah.edu AC BC00440 NAME SIMLINK DOMAIN Genetic Linkage software DESCRIPTION SIMLINK is a program for evaluating the statistical power DESCRIPTION of a proposed linkage study. AUTHOR Michael Boehnke RT - ADDRESS Department of Biostatistics, ADDRESS University of Michigan, ADDRESS USA CONTACT boehnke@umich.edu SITE WWW Server at URL http://www.sph.umich.edu/group/statgen/software SITE-CONTACT boehnke@umich.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/RHMAP_SIMLINK SITE-CONTACT nethelp@ebi.ac.uk OS UNIX and DOS LANGUAGE FORTRAN 77 VOLUME - REQUIRES - AC BC00441 NAME ANALYZE DOMAIN Genetic Linkage software DESCRIPTION The ANALYZE program package simplifies for simplifying the DESCRIPTION performance of a large array of parametric and DESCRIPTION nonparametric tests for linkage and association on data DESCRIPTION entered in LINKAGE format pedigree and parameter files. DESCRIPTION This program uses MLINK, ILINK, LINKMAP, UNKNOWN, and LSP DESCRIPTION from the LINKAGE package (either regular version 5.* or DESCRIPTION FASTLINK version 2.*) and several programs to perform these DESCRIPTION statistical tests. All code is provided except LINKAGE, DESCRIPTION which you must have pre-installed DESCRIPTION on your workstation. AUTHOR J.D. Terwilliger. RT - ADDRESS Wellcome Trust Center for Human Genetics ADDRESS Windmill Road ADDRESS Headington OX3 7BN Oxford, UK CONTACT joe@well.ox.ac.uk SITE ftp anonymous ftp.well.ox.ac.uk SITE Directory /pub/genetics/analyze SITE-CONTACT joe@well.ox.ac.uk SITE ftp anonymous linkage.rockefeller.edu SITE Directory /software/analyze SITE-CONTACT wli@linkage.rockefeller.edu SITE WWW Server at URL http://linkage.rockefeller.edu/ OS Solaris, SunOS, OSF/1 LANGUAGE Pascal VOLUME - REQUIRES LINKAGE or FASTLINK, Pascal Compiler AC BC00442 NAME DISLAMB, DISMULT DOMAIN Genetic tools DOMAIN Genetic and Physical Mapping DOMAIN Genetic Linkage software DESCRIPTION Linkage Disequilibrium Analysis DESCRIPTION There are four programs included DESCRIPTION 1) DISLAMB for single locus linkage disequilibrium analysis DESCRIPTION for a multiallelic system DESCRIPTION 2) DISMULT for multilocus linkage disequilibrium analysis DESCRIPTION 3) TDTLIKE for multiallelic likelihood-based version of the DESCRIPTION TDT test for linkage in pedigree material. DESCRIPTION 4) MCNMULT for multilocus-multiallelic likelihood-based DESCRIPTION version of the McNemar test for linkage disequilibrium in DESCRIPTION pedigree material. DESCRIPTION DISLAMB and DISMULT are discribed in the documentation file DESCRIPTION diseq.doc, and TDTLIKE and MCNMULT are described in the DESCRIPTION file tdtlike.doc AUTHOR J.D. Terwilliger RA Terwilliger J.D. RT "A Powerful Likelihood Method for the Analysis of Linkage RT Disequilibrium Between Trait Loci and One or More RT Polymorphic Marker Loci."; RL Am. J. Hum. Genet. 56:777-787(1995). ADDRESS Wellcome Trust Center for Human Genetics ADDRESS Windmill Road ADDRESS Headington OX3 7BN Oxford, UK CONTACT joe@well.ox.ac.uk SITE ftp anonymous ftp.well.ox.ac.uk SITE Directory /pub/software/diseq SITE-CONTACT joe@well.ox.ac.uk SITE ftp anonymous linkage.rockefeller.edu SITE Directory /software/diseq SITE-CONTACT wli@linkage.rockefeller.edu SITE WWW Server at URL http://linkage.rockefeller.edu/ OS Solaris, SunOS, OSF/1, VMS LANGUAGE PASCAL VOLUME - REQUIRES PASCAL Compiler AC BC00454 NAME GenoCheck DOMAIN Genetic Linkage software DESCRIPTION GenoCheck, 1.0 is an error checking program designed to identify DESCRIPTION individuals and loci that are likely to contain errors. The DESCRIPTION statistical method was designed to identify typing error, but is DESCRIPTION general enough to pinpoint any unlikely genotype still DESCRIPTION consistent with Mendelian inheritance. GenoCheck was developed DESCRIPTION using FASTLINK 2.2 (modified version of LINKAGE 5.1) and uses a DESCRIPTION similar file configuration and installation procedure. The code DESCRIPTION contains checkpointing facilities that allow users to recover DESCRIPTION from crashes without having to rerun the program and comes with DESCRIPTION documentation. AUTHOR Meg Gelder Ehm RA Ehm M.G., Cottingham R.W., Kimmel M. RT "Error Detection in Genetic Linkage RT Data Using Likelihood Based Methods."; RL J. Biol. Systems 3(1):13-25(1995). RA Ehm M.G., Cottingham R.W., Kimmel M. RA "Error Detection in Genetic Linkage RT Data Using Likelihood Based Methods."; RL Submitted to Am. J. Hum. Gen. ADDRESS Rice University, Department of Statistics ADDRESS Houston, Texas USA CONTACT gelder@stat.rice.edu SITE ftp anonymous softlib.cs.rice.edu SITE Directory /pub/GenoCheck SITE-CONTACT gelder@stat.rice.edu SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/linkage_and_mapping/FASTLINK SITE-CONTACT nethelp@ebi.ac.uk OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00578 NAME PowerLinkage DOMAIN Genetic Linkage software DOMAIN Genetic and Physical Mapping DESCRIPTION Use maximum likelihood statistics to estimate recombination DESCRIPTION frequency in F2, F2:3 populations. This program can handle DESCRIPTION more complex segregation data generated in a mapping project. AUTHOR Xianfeng Chen, Reid G. Palmer RT - ADDRESS Dept. of Agronomy, Iowa State University, ADDRESS Ames, Iowa 50011, USA CONTACT xfchen@ceres-inc.com SITE WWW Server at URL http://www.public.iastate.edu/~xfchen/researchIndex.html OS windows 95/NT LANGUAGE Visual C++ version 5.00 VOLUME - REQUIRES 32 bits window application