Genetic Linkage Analysis

• Genome DataBase
• Statistical Genomics Resources
• Laboratory Information System
• Linkage & QTL Mapping
• Pedigree (Human & Animal) Linkage Tools
• Physical Mapping
• Biological Computing & Software

• Evolution & Population Genetics Educational Database (EP-GED)
• Protein Folding@Home
• Steve Knapp's Compilation of Software Reviews
• Wentian Li's Bibliography on Algorithms in Linkage Analysis
• Wentian Li's Genetic Analysis Software List
• Thomas Sicheritz's Molecular Linux
• Daniel Week's List of Documentation
• U WI BNMC Graphics & Genetics Computing Instructional BioModules

• Other Software Archives & Search Engines
• Newsgroups & Listervers
• Books and Journals

Books and Journals

• Genetics
• Genome
• Journal of Animal Science (JAS)
• Journal of Quantitative Trait Loci (JQTL)
• Weeds World (Arabidopsis)
• Pedro's List of Journals
• Other Conferences, Journals & Newsletters

• The Genetica Analysis of Quantitative Traits by MJ Kearsey and HS Pooni, Plant Genetics Group, School of Biological Sciences, U Birmingham, UK. Chapman & Hall (Feb 1996, ISBN 0-412-60980-0).
• Statistical Genomics by Ben-Hui Liu, CRC Press (1998).
• Genetics and Analysis of Quantitative Traits by Michael Lynch (U OR Ecology & Evolution) and Bruce Walsh (U AZ Ecology & Evolutionary Biology). Sinauer (1998).
• Genetic Data Analysis II: Methods for discrete population genetic data by Bruce S. Weir. Sinauer. (May 1996 ISBN 0-87893-902-4). Companion GDA software for Windows.
• Primer on Molecular Genetics (DOE) (or at ORNL)
• Bibliography, Manuals & Software Links, Genetic Linkage Analysis Web Server, Rockefeller U

• Jurg Ott (1991) Analysis of Human Genetic Linkage, 2nd ed, John Hopkins U Press.
• WA Becker (1985) Manual of Quantitative Genetics, 4th ed, Washington St U (notes).
• Mapping and Sequencing the Human Genome: Science, Ethics and Public Policy, BSCS, 830 N. Tejon Street, Suite 405, Colorado Springs, CO 80903.

Genome DataBase

• Anubis Map Manager ( or try Roslin Inst, UK)
• GenBank (NCBI)
• Genome Sequence Data Base (GSDB)
• A C. elegans (worm) DataBase (ACEDB) is a widely used organizing genomic information (from USDA NAL). See also the WWW Gateway to ACEDB (INRA, France)
• GEMMA database for genotyping, INRA, Toulouse, France
• SIGMA: System for Integrated Genome Map Assembly (NCGR)
  (see also LANL)
• Statistics of Biological Sequences, Departement of Biometrics and Artificial Intelligence, INRA, Jouy, France
• Sybase, Inc., is used by the MaizeDB, USDA-ARS, MO.
• Quickmap, by P Rigault & E Poullier, Genethon, France.

Laboratory Information System

• LabBase from The Whitehead Institute
• LabView, National Instruments
  (In use locally at Anesthesia Lab)

Linkage & QTL Mapping

• AMOVA: Analysis of Molecular Variance Laurent Excoffier, U Geneva
• Bayesian QTL / Multimapper mapping software for inbred lines.
  Sillanpaa MJ and E Arjas (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
• Block: two-point genetic linkage analysis in an arbitrarily complex pedigree structure, Claus Skaanning
• Bmapqtl: Bayesian Interval Mapping, PJ Gaffney, JM Satagopan and BS Yandell
• GDA: (discrete) genetic data analysis, Paul O. Lewis, Biology, U NM, & Bruce S. Weir, Statistical Genetics, NC St U.
• GMendel: Jim Holloway & Steve J Knapp, OR St U Crop & Soil Science. See BH Liu and SJ Knapp (1992) J Heredity 81: 407.
• Chris Haley & Knott, UK, have a package -- details?
• JoinMap: Johan W. Van Ooijen & Roeland E. Voorrips, Plant Research International, Biometris, Wageningen. See P Stam (1993) Plant J 3: 739-744.
• MapChart: Roeland E. Voorrips, Plant Research International, Wageningen.
• MapCreator
• MapDisto: genetic linkage maps with markers showing segregation distortion (Mathias Lorieux)
• Mapmaker/QTL: The Whitehead Institute, MIT. See Lander et al. (1987) Genomics 1: 174-181.
• Map Manager & Map Manager QT: KF Manly (see Mamm. Genome (1993) 4: 303-313)
• MapQTL: Johan W. Van Ooijen, Martin P. Boer, Ritsert. C. Jansen & Chris Maliepaard, Plant Research International, Biometris, Wageningen. See Plant Genome IV Abstracts, 1996.
• Mx: linkage and other genetic epidemiological analysis; Michael C. Neale, Dept. of Psychiatry, Virginia Commonwealth University.
• MCMCQTL & RevJumpQTL: JM Satagopan, BS Yandell, MA Newton and TC Osborn (1996) Markov Chain Monte Carlo Approach to Detect Polygene Loci for Complex Traits, Genetics 144, 805-816.
  JM Satagopan and BS Yandell (1998) ``Estimating the number of quantitative trait loci via Bayesian model determination,'' Submitted to J of Agricultural, Biological, and Environmental Statistics; Special Contributed Paper Session on Genetic Analysis of Quantitative Traits and Complex Diseases, Biometrics Section, 1996 Joint Statistical Meetings, Chicago, IL.
• Mendel is a database of designations for sequenced genes in individual species of plants. The purpose of these databases is to provide a common system of nomenclature for substantially similar genes across the plant kingdom.
• MQTL: simplified composite interval mapping of QTL in multiple environments, NA Tinker & DE Mather, McGill U, Canada
• MultiCrossQTL: Ahmed Rebai, MF Jourjon, P. Chabrier, B. Goffinet, B Mangin from the INRA lab of Toulouse, France
• MultiQTL (Noam Korol)
• Pig Linkage Map Drawer, Alan Archibald
• Plant Genome Research Initiative (PGRI) and Genome-Map-Assisted Plant Breeding (GMAPB), Ben-Hui Liu, Forestry & Statistics, NC St U.
• PLABQTL & PLABSTAT: HF Utz & AE Melchinger, Institut fuer Pflanzenzuechtung, Saatgutforschung und Populationsgenetik, U Hohenheim, Stuttgart, Germany
  See Utz & Melchinger (1996) PLABQTL: A program for composite interval mapping of QTL, JQTL
• QGene: James C. "Clare" Nelson, Department of Plant Breeding and Biometry, Cornell U
  "QGene: Macintosh Software for QTL Detection and Management", Plant Genome IV, San Diego, 1996.
• QTL Cafe: G.G.Seaton, U Birmingham, UK
• QTL Cartographer: Chris Basten, Bruce S. Weir & Zhao-Bang Zeng, Program in Statistical Genetics, Department of Statistics, NC St U.
• QTL Express: Peter Visscher, Institute of Cell, Animal and Population Biology, University of Edinburgh
• Pseudomarker: Saunuk Sen and Gary Churchill, Jackson Labs.
• RAPDistance: Australia Nat U
• R/QTL and R/QTLSim, Karl Broman, Johns Hopkins Biostatistics.

• Genetic Linkage Analysis Web Server, Rockefeller U
• JM Satagopan, BS Yandell, MA Newton and TC Osborn (1996) Markov Chain Monte Carlo Approach to Detect Polygene Loci for Complex Traits, Genetics 144, 805-816.

Pedigree (Human & Animal) Linkage Tools

• ANIMAP, Dahlia Nielsen and GenMark group. half-sib family. See Genetics (1995) 139: 907-920.
• Affected Pedigree Member (APM), by Kenneth Lange, DE Weeks & M Schroeder, U Pittsburgh
• CRI-MAP, by Phil Green, U WA Seattle.
• GeneHunter: Complete multipoint linkage analysis, including haplotyping. Kruglyak, Daly, Reeve-Daly, & Lander (1996) Am J Hum Genet 58, 1347-1363.
• Genetics Analysis Package (GAP), Epicenter Software, J Buckley, U So CA
• Genetic Epidemiology (GenEpi), Molecular Biology Computation Resource (MBCR), Leif Peterson, Baylor College of Medicine
• HOMOZ homozygosity mapping, quantifying inbreeding. Focus on affected individual with recessive allele of gene. From The Whitehead Institute, MIT.
• Linkage & FastLink, originally by GM Lathrop & JM Lalouel; faster version by RW Cottingham Jr, RM Idury & AA Schaffer.
• LIPED, Jurg OTT, GDB
• Pedigree Analysis Package (PAP), by Sandra Hasstedt, U UT. (Transfer instructions may be obtained by sending an EMPTY e-mail message to info@corona.med.utah.edu with the entry 'pap' as subject.
• Segregation and Linkage analysis for Pedigrees (SALP), by Chris Stricker, Institute of Animal Science, ETH, Zurich, Switzerland; Rohan L. Fernando, Institute of Animal Science, U IL, Urbana-Champaign; and Robert C. Elston, Department of Epidemiology & Biostatistics, Case Western Reserve U, Cleveland, OH.
• Statistical Analysis for Genetic Epidemiology (SAGE), RC Elston, LA St U Medical Center (now at Department of Epidemiology & Biostatistics, Case Western Reserve U, Cleveland, OH)
• Vitesse: computes likelihoods with the functionality of the LINKMAP and MLINK. O'Connell & Weeks (1995) Am J Hum Genet suppl 57, A199; O'Connell & Weeks (1995) Nature Genetics 11, 402-408.

Coming...

• Rohan Fernando, IA St U: complicated pedigree structure in animal breeding.
• Ina Hoerschle, VPI: gibbs sampling

Physical Mapping

• GenoGraphics is a fairly generic tool that facilitates the creation of linear genetic and physical maps. By Dave zawada@athens.eid.anl.gov.
• GeneFinder: neural network
  Phil Green, U WA Seattle.
• GeneJoin and IPLab Spectrum. T Ried, A Baldini, TC Rand and DC Ward (1992) PNAS USA 89: 1388-1392.
• Mendel and Fisher: complex segregation analysis
  K Lange, Weeks, M Boehnke (1988) Genetic Epidemiology 5: 471-472. Program reviews in Hopper and Marazita (1988) Genet. Epid. 5: 473-476. Contact Kenneth Lange, Biostatistics, U MI School of Public Health.
• RHMAP,RH2PT,RHMINBRK,RHMAXLIK
  Michael Boehnke, Kenneth Lange, David R Cox (1991) Am J Hum Gen 49: 1174-88. Contact Michael Boehnke, Biostatistics, U MI School of Public Health

• See also programs highlighted in Lynch & Walsh book