- MADELINE
- full name:
- version: 0.935 (July 2004)
- descriptions: Madeline is a program designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. In addition to converting pedigree and marker data into various formats required by linkage analysis software, Madeline also provides useful functionality for querying pedigree data sets and drawing pedigrees.
- Authors: Edward Trager (email: ehtrager@umich.edu)
- web/ftp: http://eyegene.ophthy.med.umich.edu/
- source code language: C
- operating systems: UNIX (Solaris/FreeBSD/OpenBSD/MacOS), MS-Windows, Cygwin, Linux,
- executables: madeline
- reference: http://eyegene.ophthy.med.umich.edu/madeline-0.935/
- MADMAPPER
- full name:
- version: September 2005
- descriptions: suite of Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups. MadMapper_RECBIT analyses raw marker scores for recombinant inbred lines. MadMapper_RECBIT generates pairwise distance scores for all markers, clusters based on pairwise distances, identifies genetic bins, assigns new markers to known linkage groups, validates allele calls, and assigns quality classes to each marker based on several criteria and cutoff values. MadMapper_XDELTA utilizes new algorithm, Minimum Entropy Approach and Best-Fit Extension, to infer linear order of markers. MadMapper_XDELTA analyzes two-dimensional matrices of all pairwise scores and finds best map that has minimal total sum of differences between adjacent cells (map with lowest entropy). MadMapper is freely available at http://www.atgc.org/XLinkage/MadMapper/
- authors: Alexander Kozik (UC Davis Genome Center)
- web/ftp: http://www.atgc.org/XLinkage/MadMapper/
- source code language: Python
- operating systems:
- executables: MadMapper_RECBIT, MadMapper_XDELTA
- reference:
- MAGIC
- full name: Marker And Gene Interpolation and Correlation
- version: 1.0
- descriptions:
- authors: Claire Simpson (c.simpson@iop.kcl.ac.uk), Ammar Al-Chalabi (ammar@iop.kcl.ac.uk), John Powell (john.powell@iop.kcl.ac.uk)
- web/ftp: http://cogent.iop.kcl.ac.uk/MaGIC.cogx
- source code language: Microsoft Visual Foxpro
- operating systems: MS-Windows (95/98/NT/2000/XP)
- executables:
- reference: CL Simpson, VK Hansen, PC Sham, A Collins, JF Powell, A Al-Chalabi (2004), "MaGIC: A program to generate targeted marker sets for genome-wide association studies", BioTechniques, 37:996-999.
- MAIA
- full name:
- version: 1.0 (Jan 2000)
- descriptions: complex segregaton analysis in animal pedigrees
- authors: Yurii Aulchenko (email: yurii@bionet.nsc.ru)
- web/ftp: http://mga.bionet.nsc.ru/soft/maia-1.0/
- source code language:
- operating systems:
- executables:
- reference:
- MAKEPED
- full name: MAKE PEDfiles
- alias: LINKAGE/MAKEPED
- version:
- descriptions: part of the LINKAGE auxiliary program
- authors: Peter Cartwright (University of Utah, now Cimarron Software pc@cimsoft.com )
- web/ftp: ftp://linkage.rockefeller.edu/software/linkage
- source code language: C and Pascal
- operating systems: UNIX, VMS, MS-DOS, OS2
- executables:
- reference:
- MALDSOFT
- full name:
- version: 1.0
- descriptions: MALDSoft is a program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed population; additional 'learning' samples from the parental populations are helpful.
- authors: Giovanni Montana, Jonathan Pritchard (email: jpritcha@genetics.uchicago.edu)
- web/ftp: http://pritch.bsd.uchicago.edu/software/maldsoft_download.html
- source code language:
- operating systems: UNIX, Linux, MS-Windows (DOS/Window...)
- executables:
- reference: G Montana, JK Pritchard (2004), "Statistical tests for admixture mapping with case-control and cases-only data", American Journal of Human Genetics, 75:771-789.
- MAMA
- full name: Multivariate Association Mapping Algorithms
- version:
- descriptions:
- authors:
- web/ftp: http://polymorphism.ucsd.edu/cgi-bin/PRL/mama/mama.cgi
- source code language:
- operating systems: web-based
- executables:
- reference:
- MANTEL-STRUCT
- full name:
- version:
- descriptions: tests for population structure through the use of Mantel tests
- authors: Mark Miller (email: mark.miller@usu.edu)
- web/ftp: http://www.marksgeneticsoftware.net/
- source code language:
- operating systems: MS-Windows
- executables:
- reference: Miller (1999), "MANTEL-STRUCT: a program for the detection of population structure via mantel tests", Journal of Heredity, 90:258-259.
- MAP/MAP+/MAP+H/MAP2000
- full name: (MAP+H is the radiation Hybrid module of MAP+)
- version:
- descriptions: multiple pairwise linkage analysis under interference
- authors:
A Collins
(email: arc@southampton.ac.uk ),
D. Shields,
NE Morton (University of Southampton, UK) - web/ftp:
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/map
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/map+
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/map+h
http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/map2000 - source code language: FORTRAN
- operating systems: UNIX(SunOS/..)
- executables: map
- reference:
Morton, Andrew (1989),
Annals of Human Genetics, 53:263-269.
Morton, Collins (1990), Annals of Human Genetics, 54:103-106.
Shields, Collins, Buetow, Morton (1991), Proceddings of the National Academy of Sciences , 88:6501-6505.
- MAPCHART
- full name: Windows software for the graphical presentation of linkage maps and QTLs
- version: 2.2
- descriptions: Produces charts of genetic linkage and QTL data. The charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files. Many options to adapt the charts to different purposes. Can produce graphic files (enhanced windows metafile format) which can be enhanced with other MS-Windows software.
- Authors: Roeland E Voorrips (Plant Research International, Wageningen, The Netherlands) (email: r.e.voorrips@plant.wag-ur.nl)
- web/ftp: http://www.biometris.wur.nl/uk/Software/MapChart/
- source code language: Delphi
- operating systems: MS-Windows (95/98/ME/NT4.0/2000)
- executables:
- reference:
RE Voorrips (2001), "MapChart version 2.0: Windows software for the
graphical presentation of linkage maps and QTLs", Plant Research
International, Wageningen, Netherlands.
Voorrips (2002), "MapChart: Software for the graphical presentation of linkage maps and QTLs", Journal of Heredity, 93(1):77-78.
- MAPCREATOR
- full name:
- version: 4.0
- descriptions: create gene maps using either radiation hybrid data or linkage data
- authors: Wes Barris, Rachel Hawken
- web/ftp: http://www.wesbarris.com/mapcreator/
- source code language: Perl
- operating systems:
- executables:
- reference:
- price: Postscript ($69 USD), Image ($69 USD), both ($99 USD)
- MAPDISTO
- full name:
- version: v1.7.0 (October 2007)
- descriptions: MAPDISTO is a program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes.
- authors: Mathias Lorieux (m.lorieux@cgiar.org)
- web/ftp: http://mapdisto.free.fr/
- source code language: MS-Excel
- operating systems:
- executables:
- reference:
- MAPDRAW
- full name:
- version: 2.2
- descriptions: MAPDRAW draws genetic linkage maps on PC same as what MAPMAKER does on Mac.
- authors: Renhu Liu (email: liurenhu@21cn.com)
- web/ftp:
http://www.nslij-genetics.org/soft/mapdraw.v2.2.xls
ftp://brassica.hzau.edu.cn
ftp://211.69.140.177 - source code language: Microsoft Visual Basic, Excel macro
- operating systems: MS-Windows
- executables:
- reference: Liu, Meng (2003), "MapDraw: a microsoft excel macro for drawing genetic linkage maps based on given genetic linkage data", Heraditas (Beijing), 25(3):317-321.
- MAPINSPECT (see also GGT )
- full name:
- version: May 2002 (previously called MAPCOMP)
- descriptions: MAPINSPECT can be used to compare linkage maps obtained from different sources/populations/etc.. It will draw the linkage maps and look for common marker names, these are then connected in the drawing with dashed lines. All neighboring maps are compared in this way. Images can be printed and saved. Orders of the MAPs (ie which map is compared with which other map) can be changed and maps can be flipped (right mouse button). remark: MapComp bears close relationships with the GGT software package
- Authors: Ralph van Berloo, Wageningen University, The Netherlands (email: Ralph.vanberloo@pv.dpw.wau.nl)
- web/ftp: http://www.dpw.wau.nl/pv/PUB/MapComp/
- source code language: Delphi Pascal
- operating systems: MS-Window (32-bit)
- executables: MapComp.exe
- reference:
- MAPL
- full name: MAPping and QTL analysis
- version: March 2004
- descriptions: The programs allow a user to get results on segregation ratio, linkage test, recombination value, grouping of markers, ordering of markers by metric multidimensional scaling, drawing map and graphical genotype. ALso QTL analysis by interval mapping and ANOVA are possible.
- Authors: Ukai Tasuo, Ohsawa Ryo, Saito Akira, Hayashi Takeshi, Yasuo Ukai (University of Tokyo, Japan) (email: tkawai@lbm.ab.a.u-tokyo.ac.jp)
- web/ftp:
http://lbm.ab.a.u-tokyo.ac.jp/software.html
http://lbm.ab.a.u-tokyo.ac.jp/~ukai/mapl98.html - source code language: Visual Basic (V5, professional)
- operating systems: MS-Windows (95/98)
- executables:
- reference: Yasuo, Ryo, Akira, Takeshi (1995), "MAPL: a package of computer programs for construction of DNA polymorphismlinkage maps and analysis of QTL" (in Japanese), Breeding Science, 45(1):139-142.
- MATLINK
- full name:
- version:
- descriptions: A MATLAB utility for estimating genetic linkage in exotic line-cross mating designs
- authors: J Clare Nelson (Kansas State University)
- web/ftp: http://coding.plantpath.ksu.edu/~jcn/MatLink.html
- source code language: MATLAB
- operating systems:
- executables:
- reference:
- MDBLOCKS
- full name: Minimum Description length method for haplotype BLOCKS
- version:
- descriptions: Using the mimimum description length model to delineate haplotype blocks
- authors: Eric C. Anderson and John Novembre (UC Berkeley)
- web/ftp: http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/
- source code language:
- operating systems:
- executables:
- reference: Anderson, Novembre (2003), "Finding haplotype block boundaries by using the minimum description length criterion", American Journal of Human Genetics, 73:336-354.
- MAPMAKER/EXP (see also MMDRAWER)
- full name:
- version: 3.0 (1992)
- descriptions:
- authors: Eric Lander, Phil Green, J. Abrahamson, A. Barlow, Mark Daly, Steve Lincoln, L. Newburg (Whitehead Institute)
- web/ftp:
http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/
http://www-genome.wi.mit.edu/genome_software - source code language: C
- operating systems: UNIX, VMS, MS-DOS, MacOS
- executables: mapmaker
- reference:
Lander et al, Genomics,1,174-181 (1987).
online tutorial (version 3.0, 1987-1993)
- MAPMAKER/HOMOZ
- full name: homozygosity mapping
- version: May 1995
- descriptions: calculates multipoint lod scores in pedigrees with inbreeding loops
- authors:
Leonid Kruglyak
(email: leonid@genome.wi.mit.edu),
Mark Daly (email: mjdaly@genome.wi.mit.edu),
Eric Lander (email: lander@genome.wi.mit.edu ) - web/ftp: ftp://ftp-genome.wi.mit.edu/distribution/software/homoz
- source code language: C
- operating systems: UNIX
- executables:
- reference:
Kruglyak, Daly, Lander (1995),
American Journal of Human Genetics, 56:519-527.
manual (in postscript)
- MAPMAKER/QTL
- full name:
- version: new version in April 1995
- descriptions:
- authors: Eric Lander, Phil Green, J. Abrahamson, A. Barlow, Mark Daly, Steve Lincoln, L. Newburg (Whitehead Institute)
- web/ftp:
http://www-genome.wi.mit.edu/genome_software
ftp://ftp-genome.wi.mit.edu/distribution/software/newqtl" and ftp://ftp-genome.wi.mit.edu/distribution/software/mapmaker3 - source code language: C
- operating systems: UNIX, VMS, MS-DOS, MacOS
- executables:
- reference:
Lander et al, Genomics,1,174-181 (1987).
online tutorial and reference manual (v1.1, 1993)
- MAPMAKER/SIBS (see also GENEHUNTER)
- full name:
- version : 2.1 (Dec 1996)
- descriptions:
- authors:
Leonid Kruglyak
(email: leonid@genome.wi.mit.edu),
Mark Daly (email: mjdaly@genome.wi.mit.edu),
Eric Lander (email: lander@genome.wi.mit.edu ) (Whitehead Institute) - web/ftp: ftp://ftp-genome.wi.mit.edu/distribution/software/sibs
- source code language: C
- operating systems: UNIX
- executables: sibs
- reference:
Kruglyak, Lander (1995),
American Journal of Human Genetics, 57:439-454.
the changes from version 1.1 to 2.0 .
manual (in postscript)
- MAP MANAGER QT
- full name:
- version : QTb29 (August 2000)
- descriptions: A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping.
- authors: K.F. Manly
- web/ftp: http://www.mapmanager.org/mmQT.html
- source code language: Pascal
- operating systems: MacOS
- executables:
- reference: Manly and Olsen, Mammalian Genome, 10:327-334 (1999)
- MAP MANAGER QTX
- full name:
- version : QTXb20 (April 2004)
- descriptions: A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals. A completely rewritten cross-platform version of Map Manager QT with enhanced analysis functions.
- Authors: KF Manly, RH Cudmore, Jr., and JM Meer
- web/ftp: http://www.mapmanager.org/mmQTX.html
- source code language: C++ and cross-platform code from XVT
- operating systems: MS-Windows, MacOS
- executables:
- reference: Manly, Cudmore, and Meer, Mammalian Genome, in press (2001).
- MAPPOP
- full name:
- version: 1.0 (Jan 2000)
- descriptions: selects high resolution mapping subsamples and performs bin mapping
- Authors: Dan Brown, Todd Vision (email: tjv@bio.unc.edu)
- web/ftp: http://www.bio.unc.edu/faculty/vision/lab/mappop/
- source code language: MatLab
- operating systems: UNIX, MS-Windows, MacOS, etc
- executables:
- reference:
Vision, Brown, Shmoys, Durrett, Tanksley (2000),
"Selective Mapping: A strategy for optimizing the construction
of high-density linkage maps",
Genetics, 155: 407-420
Brown, Vision, Tanksley (2000), "Selective mapping: A discrete optimization approach to selecting a population subset for use in a high-density genetic mapping project", Proceedings of the 11th Annual {ACM-SIAM} Symposium on Discrete Algorithms, pp.419-428.
Xu, Zou, Vision (2005), "Improving QTL mapping resolution in experimental crosses by the use of genotypically selected samples", Genetics, 170, 401-408.
- MAPQTL
- full name: Software for the calculation of QTL positions on genetic maps
- version: 5 (October 2005)
- descriptions: Mapping of quantitative trait loci (QTLs) for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, full-sib family of outbreeders. Analyses: interval mapping, composite interval mapping, nonparametric mapping, automatic cofactor selection, permutation test for interval mapping. QTL charts. Everything available in an intuitive MS-Windows user interface.
- authors: Johan W Van Ooijen, Martin P Boer, Ritsert C Jansen, Chris Maliepaard (Plant Research International, Biometris, Wageningen, Netherlands) (email: mapping@biometris.nl)
- web/ftp: http://www.mapqtl.nl
- source code language: ANSI C, Delphi
- operating systems: MS-Windows (95/98/ME/NT4.0/2000)
- executables:
- reference: JW Van Ooijen, MP Boer, RC Jansen, C Maliepaard (2002), "MapQTL (tm) 4.0: Software for the calculation of QTL positions on genetic maps", Plant Research International, Wageningen, Netherlands; JW Van Ooijen, C Maliepaard (1996), "MapQTL Version 3.0: Software for the Calculation of QTL Positions on Genetic Maps", Plant Genome IV (1996) ( http://www.intl-pag.org/4/abstracts/p316.html); JW Van Ooijen, C Maliepaard (1996), "MapQTL Version 3.0: Advanced QTL Mapping Software", Plant Genome IV (1996) ( http://www.intl-pag.org/4/abstracts/c9.html).
- MCLEEPS (see also PANGAEA)
- full name: Monte Carlo Likelihood Estimation of Effective Population Size
- version: 1.1 (September 2001)
- descriptions:
- Authors: Eric Anderson (email: eriq@cqs.washington.edu , University of Washington) and Ellen Williamson (University of California at Berkeley)
- web/ftp:
http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml
http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm - source code language: C++
- operating systems: UNIX, MacOS
- executables:
- reference: Anderson, Williamson, Thompson (2000), "Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples", Genetics, 156:2109-2118.
- MCQTL
- full name: Multi-Cross QTL mapping
- version: v4.0
- descriptions: The aim of the MCQTL software package is to perform QTL mapping in multi-cross designs. It allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible.
- authors: Marie-Françoise Jourjon, Sylvain Jasson, Jacques Marcel, Baba Ngom, Brigitte Mangin (email: brigitte.mangin@toulouse.inra.fr)
- web/ftp: http://carlit.toulouse.inra.fr/MCQTL/
- source code language: Java, C++
- operating systems: UNIX, Linux
- executables:
- reference: Jourjon, Jasson, Marcel, Ngom, Mangin (2005), "MCQTL: Multi-allelic QTL mapping in multi-cross design", Bioinformatics, 21:128-130.
- MEGA2
- full name: a Manipulation Environment for Genetic Analyses
- version: 3.0 R9 (July 2006)
- descriptions: Mega2 uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts).
- authors: Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill, Daniel E Weeks
- web/ftp: http://watson.hgen.pitt.edu/register/
- source code language: C
- operating systems: UNIX (Solaris, Silicon Graphics, OSF1, MacOS X), Linux, MS-Windows, MacOS(X)
- executables: mega2
- reference:
Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE
(1999), "Mega2, a data-handling program for facilitating genetic
linkage and association analyses" (abstract),
American Journal of Human Genetics, 65:A436
Mukhopadhyay, Almasy, Schroeder, Mulvihill, Weeks (2005), "Mega2: data-handling for facilitating genetic linkage and association analyses", Bioinformatics, 21(10):2556-2557.
online documentation: http://watson.hgen.pitt.edu/docs/mega2_html/mega2.html
FAQ-O-MATIC: http://watson.hgen.pitt.edu/fom-serve/cache/2.html
- MENDEL
- full name:
- version: 7.0.0 (expire April 2008)
- descriptions: genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems.
- authors: Kenneth Lange (UCLA), Daniel Weeks (Pittsburgh), M. Boehnke
- web/ftp: http://www.genetics.ucla.edu/software/mendel5
- source code language: FORTRAN77
- operating systems:
- executables:
- reference:
Lange, Weeks, Boehnke (1988),
Genetic Epidemiology, 5:471-471.
module USERM14: Stringham, Boehnke, Am. J. Hum. Genet. 59, 946-950 (1996).
Lange, Cantor, Horvath, Perola, Sabatti, Sinsheimer, Sobel (2001), Am. J. Hum. Genet. 69(suppl), A1886.
- MENDELSOFT
- full name:
- version: 0.5b (July 2007)
- descriptions: Identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes.
- authors: M Sanchez, Simon de Givry (INRA, Centre de recherches de Toulouse, Station de biométrie et d'intelligence artificielle, France) (email: degivry@toulouse.inra.fr), T Schiex
- web/ftp: http://www.inra.fr/mia/T/MendelSoft/
- source code language: C++
- operating systems: UNIX, Linux/Cygwin, MS-Windows, MacOS
- executables:
- reference: Sanchez, de Givry, Schiex (2007), "Mendelian error detection in complex pedigrees using weighted constraint satisfaction techniques", Constraints, to appear.
- MERLIN
- full name: Multipoint Engine for Rapid Likelihood INference
- version: 1.0.1
- descriptions: Merlin carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels.
- Authors: Goncalo Abecasis (email: goncalo@umich.edu )
- web/ftp:
http://www.sph.umich.edu/csg/abecasis/Merlin
http://www.sph.umich.edu/csg/abecasis/Merlin/download - source code language: C++
- operating systems: UNIX. LINUX
- executables: merlin, pedstats, pedwipe
- reference: Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002), "Merlin-rapid analysis of dense genetic maps using sparse gene flow trees", Nature Genetics, 30:97-101.
- MFLINK
- full name: (nearly) model-free linkage analysis
- version:
- descriptions:
- authors: Dave Curtis, (email: dcurtis@hgmp.mrc.ac.uk) P.C. Sham
- web/ftp:
http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html
ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/statgen/dcurtis/ - source code language: C
- operating systems:
- executables:
- reference: Curtis, Sham (1995), American Journal of Human Genetics, 57:703-716.
- MGA-MAPF2
- full name:
- version:
- descriptions: map QTLs in F-2 intercross in model organisms
- authors:
- web/ftp: http://mga.bionet.nsc.ru/soft/mgamapf2/
- source code language: FORTRAN
- operating systems: MS-DOS, MS-Windows (95/98/NT)
- executables:
- reference:
- MIDAS
- full name: Multiallelic Interallelic Disequilibrium Analysis Software
- version: 1.0
- descriptions: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
- authors: Tom R Gaunt, Santiago Rodriguez, Carlos Zapata, Ian NM Day
- web/ftp:
http://www.genes.org.uk/software/midas
http://www.sgel.humgen.soton.ac.uk/midas - source code language: Python
- operating systems: MS-Windows(2000/XP), Linux, MacOS
- executables:
- reference: Gaunt, Rodriguez, Zapata, Day (2006), "MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers", BMC Bioinformatics, 7:227.
- MILD
- full name: MultIallelic Linkage Disequilibrium: a program for adjusted linkage disequilibrium (LD) calculations
- version: 2.1 (2002)
- descriptions:
- authors: Yuril S Aulchenko (email: aulchenko@epib.fgg.eur.nl) (Erasmus University Medical School, The Netherlands)
- web/ftp: http://www.geneticepi.com/Research/software/software.html
- source code language:
- operating systems: UNIX, Linux
- executables:
- reference:
- MIM
- full name: Multipoint Identical-by-descent Method
- version: 1.21 (March 1996)
- descriptions: multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families.
- authors: David Goldgar, Cathryn M. Lewis (Univ. Utah). contact person: Edward Kort at edward@episun2.med.utah.edu
- web/ftp: ftp://morgan.med.utah.edu/pub/Mim
- source code language: C
- operating systems: UNIX
- executables:
- reference:
Goldgar (1990),
American Journal of Human Genetics, 47: 957-967.
Goldgar, Oniki (1992), American Journal of Human Genetics, 50:598-606.
online manual (from Wellcome Trust)
- MINSAGE
- full name: MINimal SAmple size for GEnotypes
- version:
- descriptions: calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence
- authors: Andreas Ziegler (email: koenigir@imbs.uni-luebeck.de)
- web/ftp: http://www.imbs.uni-luebeck.de/pub/minsage/index.html
- source code language:
- operating systems: MS-Windows
- executables:
- reference: HG Gregorius (1980), "The probability of losing an allele when diploid genotypes are sampled", Biometrics, 36:643-652.
- MITPENE
- full name:
- version:
- descriptions: A program for analysis of mitochondrial diseases
- authors:
- web/ftp: http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html (in Russian)
- source code language:
- operating systems:
- executables:
- reference:
- MKGST
- full name: Michael Krawczak's Genetics Software Tools, including ASP (power calculator for gene mapping using a sibpair design), ASPSHARE (rapid calculation of the expected ibd sharing at the trait locus, based upon the model), EASYPAT (calculation of likelihood ratios for single locus data, comparing specific types of simple hypotheses regarding the familial relationships involved), MUTPROF/MUTCOMP (comparison of mutation profiles), FINDSIRE (identify mothers or sires by means of the comparison of a large number of potential parents, typed at single locus DNA markers, with given infants or parent-infant duos), PATERN (calculation of paternity probabilities from the multilocus DNA profiles of trios, comprising mother, child and putative father)
- version:
- descriptions:
- Authors: Michael Krawczak
- web/ftp: http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html
- source code language:
- operating systems:
- executables: asp, aspshare,easypat, mutprof,mutcomp, findsire,patern,fingcomp,hapmax, mutpred
- reference:
- MMDRAWER
- full name:
- version: 0.2.0.0 (April 2003)
- descriptions: draw chromosome maps from the output of MAPMAKER/EXP. The output format is a Enhanced Metafile, which can be imported into most Windows-based presentation or document editing programs.
- authors: Michael Brown
- web/ftp: http://www.emboss.co.nz/products.php?pid=2
- source code language: Delphi
- operating systems: MS-Windows
- executables:
- reference:
- MLBGH
- full name: Maximum-Likelihood-Binomial analysis of affected sib-pair and sibship data extended from the GENEHUNTER program
- version: 1.0
- descriptions: an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method.
- Authors: Laurent Abel (INSERM Unit 436, Paris, France, email: abel@biomath.jussieu.fr), Bertram Muller-Myhsok (Bernhard Nocht Institute, Hamburg, Germany, email: bmm@bni.uni-hamburg.de), Anne Philippi (INSERM Unit 436, Paris, France, email: philippi@biomath.jussieu.fr)
- web/ftp:
ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)
http://genamics.com/software/downloads/mlbgh-1.0.tar.Z - source code language: C
- operating systems: UNIX
- executables: mlbgh
- reference: Abel, Muller-Myhsok (1998), American Journal of Human Genetics, 63:638-647.
- MLD
- full name:
- version: Aug 1997
- descriptions: Performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination.
- Authors: Dmitri Zaykin (email: zaykin@statgen.ncsu.edu)
- web/ftp: ftp://statgen.ncsu.edu/pub/zaykin/
- source code language: C++
- operating systems: UNIX, MS-Windows(95)
- executables: mld.x
- reference: Zaykin, Zhivotovsky, Weir, Genetica, 96:169-178 (1995).
- MLR-TAGGING
- full name: Multivariate Linear Regression TAGGING
- version: 1.1
- descriptions: MLR-TAGGING can be used for tagging SNP selection and genotype prediction
- authors: Alexander Zelikovsky (Georgia State Univ) (email: alexz@cs.gsu.edu), Jingwu Jim He (email: jingwu@cs.gsu.edu)
- web/ftp: http://alla.cs.gsu.edu/~software/tagging/tagging.html
- source code language:
- operating systems:
- executables:
- reference: He, Zelikovsky (2006), "MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression", Bioinformatics, 22(20):2558-2561.
- MOLKIN
- full name:
- version: 2.0
- descriptions: MOLKIN is a population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MOLKIN are the computation of the between individuals (and populations) molecular coancestry coefficients, the Kinship distance at individual and population levels. Additionally, users can compute with MOLKIN a set of among populations, genetic distances and F statistics from multilocus information. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation
- authors: JP Gutierrez, LJ Royo, I Alvarez, F Goyache (Universidad Complutense de Madrid, Spain)
- web/ftp: http://www.ucm.es/info/prodanim/html/JP_Web.htm
- source code language:
- operating systems:
- executables:
- reference: Gutierrez, Royo, Alvarez, Goyache (2005), "Molkin v2.0: a computer program for genetic analysis of populations using molecular coancestry information", Journal of Heredity, 96:718-721.
- MORGAN (see also PANGAEA)
- full name: MOnte caRlo Genetic ANalysis
- version: version 2.8.1 (April 2006)
- descriptions: Programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. MORGAN 2.5 replaces MORGAN 2.4.1 (June 2002) which superceded MORGAN 2.4 (February 2002) and MORGAN 2.3.2 (September, 2001). MORGAN 2.4 supercedes MORGAN 2.3 (April 2001), MORGAN 2.2 (April 2000) and MORGAN 1.1.2 (July 1999)
- authors:
For MORGAN 2.5: M A Jewett (University of Washington, email:
myrna@stat.washington.edu)
Other authors of MORGAN programs include:
EA Thompson (University of Washington)
AW George, CJ Geyer, S Guo, SC Heath, Michael Li, S Lin,
NA Sheehan, and G Snow .
- web/ftp: http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml
- source code language: C
- operating systems: UNIX (Compaq-Alpha, Solaris and others), Linux
- reference:
Thompson (1995)
"Monte Carlo in Genetic Analysis", Technical report No. 294,
Department of Statistics, University of Washington.
[postscript]
Thompson (2000) Statistical Inferences from Genetic Data on Pedigrees NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6. IMS, Beachwood, OH.
- MPDA
- full name: Microarray Pooled DNA Analyser
- version: 2.1 (March 2008)
- descriptions: MPDA is an innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.
- authors: Hsin-Chou Yang (email:hsinchou@stat.sinica.edu.tw), Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L T Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy S J Fann
- web/ftp: http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm
- source code language: MATLABR
- operating systems: MS-Windows(Windows98/2000/XP)
- executables: mpda
- reference: Yang, Huang, Li, Lin, Yu, Diccianni, Wu, Chen, Fann (2008), "MPDA: Microarray Pooled DNA Analyzer", BMC Bioinformatics, 9:196.
- MRH
- full name: Minimum Recombinant Haplotype
- version: 0.2 (May 2003)
- descriptions:
- Authors: Dajun Qian (City of Hope National Medical Center, email: dqian@coh.org)
- web/ftp: http://www-rcf.usc.edu/~gqian/software.htm (not available)
- source code language:
- operating systems: MS-Windows, UNIX(Solaris)
- executables:
- reference: Qian, Beckmann (2002), American Journal of Human Genetics, 70:1434-1445.
- MULTIDISEQ
- full name:
- version:
- descriptions: MULTIDISEQ is multipoint linkage analysis software which allows Marker-Marker LD
- authors: Tero Hiekkalinna (email: tero.hiekkalinna@helsinki.fi)
- web/ftp: http://www.helsinki.fi/~tsjuntun/multidiseq/
- source code language:
- operating systems:
- executables:
- reference: T Hiekkalinna, L Peltonen1, JD Terwilliger (2003), "MULTIDISEQ: Computer software for multipoint linkage analysis of complex traits allowing for marker-marker LD (Linkage Disequilibrium)" (abstract), American Journal of Human Genetics, suppl, 73
- MULTIMAP
- full name:
- version:
- descriptions: program for automated construction of genetic maps
- authors: Tara Matise (email: matise@biology.rutgers.edu), Mark Perlin, Aravinda Chakravarti
- web/ftp:
http://compgen.rutgers.edu/multimap/index.shtml
http://compgen.rutgers.edu/multimap/multimapdist.html - source code language: LISP
- operating systems: UNIX (Sun/Compaq-Alpha/HP..)
- executables:
- reference: Matise,Perlin, Chakravarti, Nature Genetics, 6, 384-390 (1994);
- MULTIMAPPER
- full name:
- version:
- descriptions: Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines
- authors: Mikko J Sillanpaa (mail: mjs@rolf.helsinki.fi)
- web/ftp: http://www.rni.helsinki.fi/~mjs/
- source code language: C
- operating systems:
- executables:
- reference:
Sillanpaa, Arjas (1998),
"Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data",
Genetics, 148:1373-1388.
Martinez, Thorgaard, Robison, Sillanpaa (2005), "An application of Bayesian QTL mapping to early development in double haploid lines of rainbow trout including environmental effects", Genetical Research, 86:209-221.
- MULTIMAPPER/OUTBRED
- full name:
- version: 1.1
- descriptions: Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines
- authors: Mikko J Sillanpaa (mail: mjs@rolf.helsinki.fi)
- web/ftp: http://www.rni.helsinki.fi/~mjs/
- source code language: C
- operating systems:
- executables:
- reference: Sillanpaa, Arjas (1999), "Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data", Genetics, 151:1605-1619.
- MULTIPOPTAGSELECT
- full name:
- version: 1.1
- descriptions: The program selects a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations.
- authors: Bryan N. Howie, Christopher S. Carlson, Mark J. Rieder, and Deborah A. Nickerson (University of Washington)
- web/ftp: http://droog.gs.washington.edu/multiPopTagSelect.html
- source code language: Perl
- operating systems:
- executables: multiPopTagSelect.pl
- reference: Howie, Carlson, Rieder, Nickerson (2006), "Efficient selection of tagging single-nucleotide polymorphisms in multiple populations", Human Genetics, 120(1):58-68.
- MULTISIM
- full name:
- version: 1.1
- descriptions: analyze the numbers of individuals that founded new populations following a bottleneck or founding event
- authors: Mohamed Noor (email: noor@duke.edu)
- web/ftp: http://www.biology.duke.edu/noorlab/multsim.html
- source code language:
- operating systems: MS-DOS
- executables:
- reference: Noor, Pascual, Smith (2000), "Genetic variation in the spread of Drosophila subobscura from a nonequilibrium population", Evolution, 54:696-703.
- MUTAGENESYS
- full name:
- version:
- descriptions: MutaGeneSys is a system that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: HapMap, whole-genome marker correlation data, and OMIM database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete.
- authors: Julia Stoyanovich, Itsik Pe'er (Columbia University)
- web/ftp: http://magnet.c2b2.columbia.edu/mutagenesys/
- source code language:
- operating systems:
- executables:
- reference: Stoyanovich, Pe'er (2008), "MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data", Bioinformatics, 24(3):440-442.
N - NOCOM
- full name:
- version: Aug 1992
- descriptions: estimate parameters for mixture of normal distributions
- Authors: Jurg Ott (Rockefeller University)
- web/ftp: ftp://linkage.rockefeller.edu/software/utilities
- source code language: FORTRAN
- operating systems: MS-DOS, OS2
- executables:
- reference:
Ott (1979),
"Detection of rare major genes in lipid levels",
Human Genetics, 51:79-91.
online user's guide
- NOPAR
- full name:
- version: Aug 1995
- descriptions: non-parametric linkage and association tests primarily for a quantitative trait
- authors: A Collins (email: arc@southampton.ac.uk), NE Morton. (University of Southampton, UK)
- web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/nopar
- source code language: FORTRAN
- operating systems: UNIX(SunOS)
- executables:
- reference: Collins,Morton (1995), Human Heredity, 45:311-318.
O - ONEMAP
- full name:
- version:
- descriptions: ONEMAP is an environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants.
- authors: Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza, Antonio Augusto Franco Garcia (email: aafgarci@esalq.usp.br)
- web/ftp: http://www.ciagri.usp.br/~aafgarci/OneMap/
- source code language: R
- operating systems:
- executables: load.onemap, read.outcross, extract.group, remove.marker, arbitr.rf.2pts, est.rf.2pts, modigy.rf.2pts, group, map, make.map, est.rf.3pts
- reference: Garcia, Kido, Meza, Souza, Pinto, Pastina, Leite, Silva, Ulian, Figueira, Souza (2006), "Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases", Theoretical and Applied Genetics, 112:298-314.
- OSA
- full name: Ordered Subset Analysis
- version: 2.1
- descriptions: OSA allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.
- authors: William Duren, Mike Boehnke, Elizabeth Hauser
- web/ftp: http://wwwchg.duhs.duke.edu/software/osa.html
- source code language: C++
- operating systems: UNIX(Solaris), Linux
- executables: osa2.0
- reference:
ER Hauser, MP Bass, ER Martin, RM Watanabe, WL Duren, M Boehnke (2001),
Am J Hum Genet, suppl 69:529.
ER Hauser, RM Watanabe, WL Duren, MP Bass, CD Langefeld, M Boehnke (2003), "Ordered subset analysis in genetic linkage mapping of complex traits", Genetic Epidemiology, to appear.
- OSIRIS
- full name:
- version: 1.1
- descriptions: OSIRIS is a tool for the retrieval of articles from MEDLINE related to the sequence variants reported for a human gene. The variations considered are single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indel), microsatellite, and named variations (e.g. Alu sequences).
- authors: Julio Bonis , Laura Ines Furlong Ferran Sanz (University of Pompeu Fabra, Spain) (email: fsanz@imim.es)
- web/ftp: http://ibi.imim.es/osirisform.html
- source code language:
- operating systems:
- executables:
- reference: Bonis, Furlong, Sanz (2006), "OSIRIS: a tool for retrieving literature about sequence variants", Bioinformatics, 22(20):2567-2569.
P - PANGAEA (see also BOREL, ECLIPSE, HARDY, INSEGT, LOKI, MCLEEPS, MORGAN, PEDFIDDLER, PEDPACK )
- full name: Pedigree ANalysis for Genetics (And Epidemiological Attributes)
- version:
- descriptions:
Collection of nine packages for genetic analysis;
the original four BOREL, HARDY, MORGAN and PEDPACK, plus INSEGT, LOKI, MCLEEPS, PEDFIDDLER, and ECLIPSE - Authors: many authors: see individual packages. managed by EA Thompson (University of Washington, email: thompson@stat.washington.edu).
- web/ftp: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml
- source code language: C or C++
- operating systems: UNIX (Compaq, Solaris, and others), Linux
- executables:
- reference:
- PAP
- full name: Pedigree Analysis Package
- version: 6.0 (December 2006)
- descriptions: it can perform (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models
- authors:
Sandra Hasstedt (University of Utah,
email:
sandy@genetics.utah.edu)
Peter Cartwright contributed to versions 2 and 3; many others contributed to version 1 (University of Utah) - web/ftp: http://hasstedt.genetics.utah.edu/
- source code language: FORTRAN 77
- operating systems: UNIX
- executables: preped, descstat, prepap,simul, papdr (with 8 options),gpe
- reference: manual (version 5, PDF) online manual (version 4) (from Wellcome Trust)
- PARENTE
- full name:
- version: 1.2 (February 2003)
- descriptions: parentage inference using molecular data from diploid codominant markers
- authors: Stephanie Blanc-Manel (email: stephanie.manel@ujf-grenoble.fr)
- web/ftp: http://www2.ujf-grenoble.fr/leca/membres/manel.html
- source code language:
- operating systems:
- executables:
- reference: Cercueil, Bellemain, Manel (2002), "PARENTE: computer program for parentage analysis", Journal of Heredity, 93:458-459.
- PAWE
- full name: Power for Association With Error
- version: Dec 2002
- descriptions: Power and sample size calculations for genetic case-control association studies allowing for errors
- authors: Derek Gordon (email: gordon@linkage.rockefeller.edu), assisted by Michael Nothnagel
- web/ftp: http://linkage.rockefeller.edu/pawe/
- source code language:
- operating systems:
- executables:
- reference: Gordon, Finch, Nothnagel, Ott (2002), Human Heredity, 54:22-33.
- PAWE-3D
- full name: Power for Association With Error in 3D
- version:
- descriptions:
- authors: D Gordon, C Haynes, J Blumenfeld, SJ Finch
- web/ftp: http://linkage.rockefeller.edu/pawe3d/
- source code language:
- operating systems: web-based
- executables:
- reference: Gordon, Haynes, Blumenfeld, Finch (2005), "PAWE-3D: visualizing Power for Association With Error in case/control genetic studies of complex traits", Bioinformatics, 21:3935-3937.
- PBAT (see also FBAT )
- full name: Power calculation of family-Based Association Tests
- version: 1.2 (November 2003)
- descriptions: PBAT is an interactive software package that provides tools for the design and the data analysis of family-based association studies.
- authors: Christoph Lange (email: clange@hsph.harvard.edu) (Harvard Univ).
- web/ftp: http://www.biostat.harvard.edu/~clange/default.htm
- source code language:
- operating systems:
- executables:
- reference:
C Lange et al (2003), "Using the noninformative families in family-based
association tests: A powerful new testing strategy",
American Journal of Human Genetics, 801-811.
C Lange et al (2004) "PBAT: tools for family-based association studies", American Journal of Human Genetics, in press.
Steen, Lange (2005), "PBAT: A comprehensive software package for genome-wide association analysis of complex family-based studies", Human Genomics, 2(1):67-69.
Hoffmann, Lange (2006), "P2BAT: a massive parallel implementation of PBAT for genome-wide association studies in R", Bioinformatics, 22:3103-3105.
- PDA
- full name: Pooled DNA Analyzer
- version:
- descriptions: a tool for analyses of pooled DNA data
- authors: Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann (Institute of Biomedical Sciences, Academia Sinica, Taiwan)
- web/ftp: http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm
- source code language:
- operating systems:
- executables:
- reference: Yang, Pan, Lin, Fann (2006), "PDA: pooled DNA analyzer", BMC Bioinformatics, 7:233.
- PDPSYS
- full name: Pedigree Data Processing SYStem
- version: 1.0 (November 1998)
- descriptions: PDPSys is a Windows-based system designed for pedigree data management, providing a graphical interface for pedigree construction and output.
- Authors: Fil Quiaoit (Fred Hutchinson Cancer Research Center, email: fquiaoit@fhcrc.org)
- web/ftp: http://cougar.fhcrc.org/software.php
- source code language: Visual Basic, MS-Access
- operating systems: MS-Windows (95)
- executables: pdpsys
- reference:
- PDT
- full name: pedigree disequilibrium test
- version: 5.1
- descriptions: The PDT analysis program allows the user to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets.
- Authors: Eden Martin (Duke Univ)
- web/ftp: http://www.chg.duke.edu/software/pdt.html
- source code language:
- operating systems: UNIX(Solaris)
- executables:
- reference: Martin, Monks, Warren, Kaplan (2000), American Journal of Human Genetics, 67:146-154.
- PED
- full name: PEdigree Drawing software
- version: 5.1.0 (October 2006)
- descriptions: Powerful pedigree drawing program with two drawing modes: Input mode for fast and automatic drawing; edit mode for text annotations, legends, special symbols. Both input and edit mode provide auto numbering, auto resizing of symbols and fonts, and zooming. PED 4.2a complies with the "Recommendations for standardized human pedigree nomenclature" proposed by the PSTF (Bennet RL et al (1995), American Journal of Human Genetics, 56:745-752). Apart from fully sizeable printed output, pedigrees can be exported as metafiles to virtually any Windows word processor or drawing program.
- Authors: Hansjoerg Plendl (email: plendl@medgen.uni-kiel.de )
- web/ftp:
http://www.medgen.de/index.html
http://www.medgen.de/ped/index.htm - source code language: Visual Smalltalk
- operating systems: MS-Windows (95/98/NT)
- executables: ped.exe
- reference: A Golla, Medizinische Genetik, 4:595-597 (1997); H Plendl, Medizinische Genetik, 1:50-51 (1998).
- price: site license US$99.
- PEDAGREE
- full name: 1.00 (February 2002)
- version:
- descriptions: a program for detecting autosomal marker Mendelian incompatibilities in pedigree data
- authors: Christine Couillault (email: kristin.c@free.fr)
- web/ftp: http://pedagree.free.fr/
- source code language: C, C++
- operating systems: UNIX, Linux, MS-Windows, MS-DOS,
- executables: pedagree
- reference:
- PEDCHECK
- full name:
- version: 1.0 (November 1998)
- descriptions: identifying all Mendelian inconsistencies in pedigree data.
- Authors: J. R. O'Connell (email: jeff@sherlock.hgen.pitt.edu )
- web/ftp: http://watson.hgen.pitt.edu/register
- source code language: C, C++
- operating systems: UNIX(SunOS/Solaris/Compaq-Alpha/SGI-IRIX/..)
- executables:
- reference: Am Soc Hum Genet annual meeting 1997
(O'Connell, Weeks, Am. J. Hum. Genet. suppl,61, A288 (1997));
O'Connell, Weeks (1998),
American Journal of Human Genetics, 63:259-266.
FAQ-O-MATIC: http://watson.hgen.pitt.edu/fom-serve/cache/8.html
- PEDFIDDLER (see also PEDPACK in PANGAEA)
- full name:
- version: 0.5 (August 2005)
- descriptions: This suite of six programs can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK.
- Authors: J C. Loredo-Osti (email: josti@bagel.epi.mcgill.ca), Kenneth Morgan (email: ken@bagel.epi.mcgill.ca); Window version adapted by Michael Li (email:lina@u.washington.edu).
- web/ftp: http://www.stat.washington.edu/thompson/Genepi/Pedfiddler.shtml
- source code language: C,C++
- operating systems: UNIX (OSF1, and Solaris 2.7, AlphaLinux) MS-Windows (XP Home/Win32/Win95), Linux
- executables:
- reference:
- PEDGENIE
- full name:
- version: 1.2 (April 2006)
- descriptions: PedGenie is a general-purpose tool to analyze association and transmission disequilibrium (TDT) between genetic markers and traits in families of arbitrary size and structure. Any size pedigree may be incorporated into this tool, from independent individuals to large genealogies. Independent individuals and families may be analyzed together.
- authors: K. Allen-Brady, J. Wong, N.J. Camp
- web/ftp: http://bioinformatics.med.utah.edu/PedGenie/index.html
- source code language: Java 1.5
- operating systems:
- executables:
- reference: Allen-Brady, Wong, Camp (2006), "PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size", BMC Bioinformatics, 7:209.
- PEDHUNTER
- full name:
- version:
- descriptions: a software package that facilitates creation and verification of pedigrees within large genealogies.
- Authors: Agarwala, Biesecker, Hopkins, Francomano, Schffer (NIH)
- web/ftp: http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html
- source code language:
- operating systems:
- executables:
- reference: Agarwala, Biesecker, Hopkins, Francomano, Schffer (1998), "Software for constructing and verifying pedigrees within large genealogies and an application to the Old Order Amish of Lancaster county", Genome Research, 8:211-221.
- PEDIGRAPH
- full name:
- version: 2.3
- descriptions: A pedigree visualization program specifically designed to draw large, complex pedigrees.
- authors: John Garbe (University of Minnesota, email: jgarbe@umn.edu), Yang Da (University of Minnesota, email: yda@umn.edu)
- web/ftp: http://animalgene.umn.edu/pedigraph/
- source code language: C,C++
- operating systems: MS-Windows, Linux
- executables: pedigraph
- reference: J Garbe, Y Da (2003), Pedigraph user manual Version 1.1. Department of Animal Science, University of Minnesota.
- PEDIGREE/DRAW
- full name:
- version: 6
- descriptions: pedigree drawing
- authors: Bennett Dyke (email: bdyke@darwin.sfbr.org ), Paul Mamelka (contact person, email: paul@darwin.sfbr.org ), J. MacCleur, Southwest Foundation for Biomedical Research
- web/ftp:
http://www.pedigree-draw.com/
ftp://www.sfbr.org/pub/pedmgt/peddrw - source code language:
- operating systems: MacOS
- executables:PedDraw
- reference: Am Soc Hum Genet annual meeting 1987 (Dyke, Mamelka, Am J. Hum Genet, suppl 41, A253 (1987))
- price: disk and user's guide: US$45; user's guide: US$20; upgrade for disk: US$15;
- PEDIGREEQUERY
- full name:
- version:
- descriptions: allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families
- authors: A Kirichenko
- web/ftp:
http://mga.bionet.nsc.ru/soft/index.html
http://mga.bionet.nsc.ru/PedigreeQuery/PedigreeQuery.html (in Russian) - source code language:
- operating systems:
- executables:
- reference: A Kirichenko (2003), "PedigreeQuery - software for pedigree drawing" (abstract), American Journal of Human Genetics, suppl
- PEDIGREE-VISUALIZER
- full name:
- version:
- descriptions:
- authors: Limsoon Wong (National University of Singapore, Singapore)
- web/ftp: http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/
- source code language:
- operating systems:
- executables:
- reference:
- PEDJAVA
- full name: PedJava
- version: 1.1
- descriptions: Allows pedigree entry and retrieval from an internet browser into a distant MS ACCESS database. Includes IP access restriction, automatic numbering of families and individuals and database consistency checks.
- Authors: Matthias Wjst (email: wjst@gsf.de), Juergen Knauth (email: woodoo@bigfoot.de )
- web/ftp: http://cooke.gsf.de/wjst/download.cfm
- source code language: JDK
- operating systems: no restriction for client, server WIN 95/NT
- executables: pedJava, pedJavaServer
- reference: in preparation
- PEDMANAGER
- full name:
- alias: MAPMAKER/PEDMANAGER
- version: 0.9 (1997)
- descriptions:
- authors: Mary Pat Daly (previously Mary Pat Reeve) (MIT/Whitehead)
- web/ftp: http://www-genome.wi.mit.edu/ftp/distribution/software/pedmanager/
- source code language: C
- operating systems: UNIX
- executables: pedprep
- reference:
- PEDPHASE
- full name:
- version: 2.0
- descriptions: inferring haplotypes from genotypes on pedigree data
- authors: Jing Li(email: jingli@eecs.cwru.edu)
- web/ftp: http://vorlon.case.edu/~jxl175/haplotyping.html
- source code language:
- operating systems: MS-Windows
- executables:
- reference:
Li, Jiang (2003),
"Effecient rule-based haplotyping algorithms for pedigree data",
Proceedings of the Seventh International Conference on Research
in Computational Molecular Biology , pp.197-206.
Li, Jiang (2004), " An exact solution for finding minimum recombinant haplotype configurations on pedigrees with missing data by integer linear programming", Proceedings of the Seventh International Conference on Research in Computational Molecular Biology , pp.101-110.
- PEDPACK (see also PANGAEA)
- full name:
- version: Version 2.2, July 1996
- descriptions: Programs for pedigree analysis, including segregation analysis, gene extinction, and pedigree graphics.
- authors:
A.W. Thomas (Versions 1.0, 3.0, 3.1)
E.A. Thompson (University of Washington, email: thompson@stat.washington.edu)
C.J. Geyer (University of Minnesota, email: charlie@stat.umn.edu) - web/ftp: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml
- source code language: C
- operating systems: UNIX(Compaq-Alpha/..)
- executables:
- reference:
Thomas, IMA J. Math Appl Med Biol, 5, 210-213 (1988)
Thomas, "Pedpack: Users' Manual", Technical report No. 99, Dept Statistics, University of Washington.
Thomas, "Pedpack: Managers' Manual", Technical report No. 100, Dept Statistics, University of Washington.
Geyer, (1988), "Software for calculating gene survival and multigene descent probabilities, and for pedigree manipulation and drawing", Technical report No. 153, Dept Statistics, University of Washington.
- PEDPLOT
- full name:
- version:
- descriptions: Pedigree Plotting Program for the Pedfile Format
- Authors: JE Stajich (email: jason@chg.mc.duke.edu), C Haynes (email: carol@chgd.mc.duke.edu), MA Pericak-Vance (Duke University Medical Center)
- web/ftp: http://www.chg.duke.edu/software/pedplot.html
- source code language: C++, Postscript
- operating systems: UNIX(Sparc-Solaris 2.5/DEC UNIX 4.0/x86-Solaris 2.6)
- executables: pedplot
- reference: Am Soc Hum Genet annual meeting 1998 (Stajich, Haynes, Pericak-Vance, Am J Hum Genet, suppl, 63,A242).
- PEDRAW/WPEDRAW
- full name: Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW)
- version: 2.5
- descriptions: a pedigree drawing program using LINKAGE data files
- authors: Dave Curtis (email: dcurtis@hgmp.mrc.ac.uk)
- web/ftp:
http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html
ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/statgen/dcurtis/ - source code language: C++
- operating systems: MS-DOS, MS-Windows, X-window
- executables:
- reference: Curtis (1990), Annals of Human Genetics, 54:365-367.
- PEDSTATS
- full name:
- version: 0.6.8
- descriptions: PEDSTATS does error checking and data summary of large or small data sets in QTDT, LINKAGE or MENDEL format. Checks for basic formatting errors, disconnected family groups, ancestor-descendant loops and can detect all Mendelian (including X-linked) inheritance errors in any pedigree without loops. Produces text and graphical (PDF) summaries of the family structure, trait and marker information of pedigree data and can break down summaries by sex, relative pair type or family. PEDSTATS also does Hardy-Weinberg testing using either a fast exact or asymptotic test and can summarize information in text or graphical PDF format. Additional features include a number of options for filtering data prior to summary and checks for inappropriate age or covariate values. Lastly, PEDSTATS can identify and trim uninformative individuals from a pedigree and rewrite the reorganized data to a new pedigree file.
- authors: Janis Wigginton (email: wiggie@umich.edu), Goncalo Abecasis (email: goncalo@umich.edu)
- web/ftp: http://www.sph.umich.edu/csg/abecasis/Pedstats/
- source code language: C,C++
- operating systems: Linux, UNIX, MS-Windows
- executables: pedstats
- reference: Wigginton, Abecasis (2005), "PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data", Bioinformatics, 21:3445-3447.
- PEDSYS
- full name:
- version: 2.0
- descriptions: a full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data.
- authors: Bennett Dyke (email: bdyke@darwin.sfbr.org ), Paul Mamelka (email: paul@darwin.sfbr.org ),
- web/ftp:
http://www.sfbr.org/sfbr/public/software/pedsys/pedsys.html
ftp://www.sfbr.org/pub/pedmgt/pedsys - source code language:
- operating systems: UNIX(SunOS,Solaris), MS-DOS, MacOS
- executables:
- reference:
- price: disks or tapes and user's manual: US$55; user's manual: US$30; disk for registered users: US$20. person to contact: Linda Freeman-Shade, Dept Genetics, Southwest Foundation for Biomedical Research, P.O. Box 760549, San Antonio, TX 78245-0549 (email: linda@darwin.sfbr.org )
- PEDVIZAPI
- full name: PEDigree VIsualiZation API
- version: 0.15 (November 2007)
- descriptions: PEDVIZAPI is a Java Api for the visual analysis of large and complex pedigrees. It provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data.
- authors: Christain Fuchsberger (email: christian.fuchsberger@eurac.edu), Mario Falchi, Lukas Forer, Peter Pramstaller
- web/ftp: http://www.pedvizapi.org/
- source code language: Java, R
- operating systems:
- executables:
- reference: Fuchsberger, Falchi, Forer, Pramstaller (2007), "PedVizApi: A Java API for the interactive, visual analysis of extended pedigrees", Bioinformatics, 24(2):279-281.
- PELICAN
- full name: Pedigree Editor for LInkage Computer ANalysis
- version:
- descriptions: It is a utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN.
- authors: Frank Dudbridge (MRC, email: frank.dudbridge@mrc-bsu.cam.ac.uk )
- web/ftp: http://www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/
- source code language: Java
- operating systems:
- executables:
- reference: F Dudbridge, T Carver, GW Williams (2004), "Pelican: pedigree editor for linkage computer analysis", Bioinformatics, 20(14):2327-2328.
- PHASE
- full name:
- version: 2.0 (Sept 2003)
- descriptions:
This program implements a new statistical method for reconstructing
haplotypes from population genotype data
new for v2: (1) the introduction of a new computational approach, resulting in much faster haplotype resolution. (2) the introduction of a new model that allows for recombination and decay of Linkage Disequilibrium (LD) with distance, which results in more accurate haplotype estimates. This model also allows the user to estimate recombination rates, and identify recombination hotspots from population genotype data. (3) the facility to perform a test for haplotype frequency differences between cases and controls. (4) more extensive output summarising the results. - Authors: Matthew Stephens (email: stephens@stat.washington.edu)
- web/ftp:
http://www.stat.washington.edu/stephens/software.html
previous site: http://www.stats.ox.ac.uk/mathgen/software.html - source code language:
- operating systems:
- executables:
- reference: Stephens, Smith, Donnelly (2001), AJHG, 68:978-989.
- PIAGE
- full name: Power of Indirect Association Studies of Gene-Environment Interactions
- version: 1.0 (March 2008)
- descriptions: The program PIAGE performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman's (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components.
- authors: Rebecca Hein (email:r.hein@dkfz-heidelberg.de), Lars Beckmann (email:l.beckmann@dkfz-heidelberg.de)
- web/ftp: http://www.dkfz.de/en/klepidemiologie/software/software.html
- source code language: R
- operating systems: MS-Windows, Linux
- executables:
- reference:
Hein, Beckmann, Chang-Claude (2008),
"Sample size requirements for indirect association studies of gene-environment interactions (GxE)",
Genetic Epidmiology, to appear.
Gauderman (2002), "Sample size requirements for matched case-control studies of gene-environment interaction", Statistics in Medicine, 21:35-50.
Kraft, Yen, Stram, Morrison, Gauderman (2007), "Exploiting gene-environment interaction to detect genetic associations", Human Heredity, 63:1141-1119.
- PLABQTL
- full name: PLAnt Breeding QTL analysis
- version:
- descriptions:
- authors: HF Utz (email: utzf@uni-hohenheim.de)
- web/ftp: https://www.uni-hohenheim.de/plantbreeding/software/
- source code language:
- operating systems:
- executables:
- reference: Utz, Melchinger (1996), "PLABQTL: A program for composite interval mapping of QTL", JAG
- PLABSIM
- full name: PLAnt Breeding SIMulation
- version: 1.0.1 (June 2005)
- descriptions:
- authors: Matthias Frisch (email: frisch@uni-hohenheim.de)
- web/ftp: http://www.uni-hohenheim.de/~frisch/software.html
- source code language: C++
- operating systems: UNIX(AIX), Linux, MS-Windows(NT)
- executables:
- reference: Frisch, Bohn, Melchinger (2000), "PLABSIM: software for simulation of marker-assisted backcrossing", Journal of Heredity, 91:86-87.
- PL-EM
- full name: Partition-Ligation EM algorithm for haplotype inference with single nucleotide polymorphisms
- version:
- descriptions:
- authors: Jun Liu, Steve Qin, Tianhua Niu (Harvard Univ)
- web/ftp: http://www.people.fas.harvard.edu/~junliu/plem/
- source code language:
- operating systems:
- executables:
- reference: Qin, Niu, Liu (2002), American Journal of Human Genetics, (letter), 71:?-?.
- PLINK
- full name:
- version:
- descriptions: a whole-genome association analysis toolset
- authors: Shaun Purcell
- web/ftp: http://pngu.mgh.harvard.edu/purcell/plink/
- source code language:
- operating systems:
- executables:
- reference: Purcell, Neale, Todd-Brown, Thomas, Ferreira, Bender, Maller, de Bakker, Daly, Sham (2007), "PLINK: a toolset for whole-genome association and population-based linkage analysis", American Journal of Human Genetics, to appear.
- POINTER
- full name:
- version:
- descriptions: for complex segregation analysis with the mixed model (major locus and polygenes).
- authors: NE Morton (University of Southampton, UK), D.C. Rao, J-M. Lalouel
- web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/pointer
- source code language: SUN FORTRAN (especially, the command "fsplit" is needed)
- operating systems: UNIX (SunOS/..)
- executables:
- reference: Morton, Rao, Lalouel, "Methods in Genetic Epidemiology" (Karger, 1983).
- POLYMORPHISM
- full name:
- version: 1.4 (June 1999)
- descriptions: calculating the heterozygosity, PIC, and LIC values for polymorphic markers
- Authors: Tianhua Niu, Sc.D. (Harvard Medical School, email: tniu@hohp.harvard.edu)
- web/ftp:
- source code language: C
- operating systems: UNIX
- executables: powerlic
- reference:
Guo, Elston (1999),
"Linkage information content of polymorphic genetic markers",
Human Heredity, 49:112-118.
Niu, Struk, Lindpaintner (2001), Human Heredity, 52(2):102-109.
- POOLSCORE
- full name:
- version:
- descriptions: a program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools
- authors: Paul McKeiger (email: paul.mckeigue@ucd.ie) (University College Dublin, Ireland)
- web/ftp: http://www.ucd.ie/genepi/pooling/poolscore.htm
- source code language: R
- operating systems:
- executables: poolscore.R
- reference:
- POOL_STR
- full name: POOLing alleles of Short Tandem Repeat markers
- version: 1.1
- descriptions:
- authors: Yurii Aulchenko, Aida Bertoli-Avella, Cornelia van Duijn (Erasmus University Medical School, The Netherlands)
- web/ftp:
http://www.geneticepi.com/Research/software/software.html
http://www.geneticepi.com/Research/software/pool_str-1.1.tar.gz - source code language:
- operating systems:
- executables:
- reference: Aulchenko, Beroli-Avella, van Duijn (2005), "A method for pooling alleles from different genotyping experiments", Annals of Human Genetics, 69(2):233-238.
- POPDIST
- full name:
- version: 1.1.2
- descriptions: POPDIST calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures
- authors: Bernt Guldbrandtsen (email: bg@genetics.agrsci.dk)
- web/ftp: http://genetics.agrsci.dk/~bg/popgen/
- source code language:
- operating systems: UNIX (AIX/IRIX/DECalpha), Linux, MacOS, MS-DOS, MS-Windows(95)
- executables:
- reference: Guldbrandtsen, Tokiuk, Loeschcke (2000), "POPDIST, version 1.1.1: a program to calculate population genetic distance and identity measures", Journal of Heredity, 91:178-179.
- POPGEN
- full name:
- version:
- descriptions: POPGEN is an R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group.
- authors: Jonathan Marchini (email: marchini@stats.ox.ac.uk)
- web/ftp:
http://www.stats.ox.ac.uk/mathgen/software.html
http://www.stats.ox.ac.uk/~marchini/software.html - source code language: R
- operating systems:
- executables: popdiv, ps, nps, treesim, simMD
- reference:
- POWER
- full name:
- version: 3.0
- descriptions: windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions).
- authors:
- web/ftp: http://dceg.cancer.gov/POWER/
- source code language:
- operating systems: MS-Window
- executables:
- reference: Garcia-Closas, Lubin (1999), "Power and sample size calculations in case-control studies of gene-environmental interactions: Comments on different approaches", American Journal of Epidemiology, 149:689-693.
- POWERMARKER
- full name:
- version: 3.25 (February 2006)
- descriptions: PowerMarker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. See analysis to check out the versatility of PowerMarker. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results.
- authors: Jack Liu
- web/ftp: http://statgen.ncsu.edu/powermarker/
- source code language:
- operating systems:
- executables:
- reference: Liu, Muse (2005), "PowerMarker: an integrated analysis environment for genetic marker analysis", Bioinformatics, 21(9):2128-2129.
- POWERTRIM
- full name:
- version:
- descriptions: automate the decision to remove objects from a pedigree with a minimum loss information
- authors: Tricia Thornton, Jonathan Haines (Venderbilt University Medical Center)
- web/ftp: http://phg.mc.vanderbilt.edu/content/powertrim
- source code language: Perl
- operating systems:
- executables:
- reference: Thornton, Haines (2003), American Journal of Human Genetics, 72:1280-1281.
- POWQ
- full name:
- version:
- descriptions: A user-friendly, graphical package for power evaluation and enhancement planning through variance component linkage analysis in a multipoint framework.
- authors: Mario Falchi (email: mario.falchi@kcl.ac.uk) Cesare Cappio Borlino
- web/ftp: http://www.twin-research.ac.uk/WebPowQ/PowQ.htm
- source code language:
- operating systems:
- executables:
- reference: Falchi and Borlino (2006), "PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies", Bioinformatics, 22(11):1404-1405.
- POWTEST
- full name:
- version:
- descriptions: Excel spreadsheet to calculate power of affected sibpairs and TDT analyses
- authors: Dave Curtis
- web/ftp: http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html
- source code language:
- operating systems:
- executables:
- reference:
- PREPLINK
- full name: MAKE PEDfiles
- alias: LINKAGE/PREPLINK
- version:
- descriptions: part of the LINKAGE auxiliary program
- authors: Peter Cartwright (University of Utah, now Cimarron Software pc@cimsoft.com )
- web/ftp: ftp://linkage.rockefeller.edu/software/linkage or
- source code language: C and Pascal
- operating systems: UNIX, VMS, MS-DOS, OS2
- executables:
- reference:
- PREST
- full name: Pedigree RElationship Statistical Test
- version: 3.0.2 (February 2005)
- descriptions: PREST is a program that detects pedigree errors in general outbred pedigrees by use of genome-screen data. When a potential pedigree error is detected, our companion program, ALTERTEST, determines which relationships are compatible with the observed genotype data. Both programs are freely available on the web.
- authors: Lei Sun, Kenneth Wilder, Mary Sara McPeek (University of Chicago)
- web/ftp: http://fisher.utstat.toronto.edu/sun/Software/Prest or previously, http://galton.uchicago.edu/~mcpeek/software/prest
- source code language: C
- operating systems: Linux, UNIX(Solaris/..)
- executables: prest.solaris, prest.linux, altertest.solaris, altertest.linux
- reference: McPeek and Sun (2000), "Statistical tests for detection of misspecified relationships by use of genome-screen data", American Journal of Human Genetics, 66:1076-1094.
- PRESTO
- full name:
- version: 1.0.1 (October 2007)
- descriptions: PRESTO performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.
- authors: Brian L Browning (email: b.browning@auckland.ac.nz)
- web/ftp: http://www.stat.auckland.ac.nz/~browning/presto/presto.html
- source code language: Java
- operating systems: MS-Windows, UNIX (Solaris/..), Linux, MacOS
- executables:
- reference:
- PROBMAX
- full name:
- version:
- descriptions: assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny
- authors: Roy Danzmann (email: rdanzman@uoguelph.ca)
- web/ftp: http://www.uoguelph.ca/~rdanzman/software/PROBMAX/
- source code language:
- operating systems:
- executables:
- reference: Danzmann (1997), "PROBMAX: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny", Journal of Heredity, 88:333.
- PROFILER
- full name:
- version:
- descriptions: A flexible tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map.
- authors: Jeff O'Connell
- web/ftp: http://www.molecular-haplotype.org/profiler/profiler_intro.htm
- source code language:
- operating systems: Linux, UNIX(Solaris)
- executables:
- reference:
- PROGENY
- full name: Progeny Software, LLC
- version: 6.8 (December 2006)
- descriptions: Fully customizable, multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms.
- authors: David Deram (Progeny Software, LLC)
- web/ftp: http://www.progenygenetics.com/
- source code language: C++ and Active X Controls
- operating systems: MS-Windows (95/98/2000/ME/NT/XP)
- executables:
- reference:
- PRT
- full name: Pedigree Reconstruction Tools
- version: 1.2
- descriptions: Partition of single generation into sibling groups
- authors: Anthony Almudevar (Dept Biostatistics and Computational Biology, University of Rochester Medical Center, email: anthony_almudevar@urmc.rochester.edu)
- web/ftp: http://www.urmc.rochester.edu/smd/biostat/Projects/Help/PC/Software_Listings.htm
- source code language:
- operating systems: MS-Windows
- executables: msg_proj
- reference: A Almudevar, C Field (1999), "Estimation of single generation sibling relationships based on DNA markers", J. Agricultural, Biological and Environmental Statistics, 4(2):136-165.
- PSEUDO
- full name:
- version: 0.3.5
- descriptions: Pseudo estimates genomewide empirical p-values for Kong and Cox tests of linkage using the replicate pool method, which for many data sets, improves upon the computational efficiency of conventional gene-dropping methods by several orders of magnitude. This allows Pseudo to handle data sets with large families and makes it particularly applicable to those situations where p-value estimation by standard methods is computationally prohibitive. Pseudo also estimates variance for reported p-values, produces graphical and text summaries of results, and is able to assess significance of multiple correlated outcomes. Pseudo is designed to work with the Merlin package and includes utilities for generating input files from standard Merlin output.
- authors: Janis Wigginton (email:wiggie@umich.edu) and Goncalo Abecasis
- web/ftp: http://www.sph.umich.edu/csg/abecasis/pseudo/download
- source code language: C,C++
- operating systems: Linux, UNIX, MacOS, MS-Windows
- executables: pseudo, scan
- reference: Wigginton, Abecasis (2006), "An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values", Genetic Epidemiology, 30(4):320-332.
- PSEUDOMARKER
- full name:
- version: 1.0.4 (October 2006)
- descriptions: PSEUDOMARKER is linkage analysis software for Joint Linkage and/or Linkage Disequilibrium Analysis. Pseudomarker can analyze different data structures jointly such as cases and controls, trios, sib pairs, sib ships and extended families.
- Authors: Tero Hiekkalinna (email: tero.hiekkalinna@helsinki.fi), Joseph D Terwilliger
- web/ftp: http://www.helsinki.fi/~tsjuntun/pseudomarker/
- source code language: C,C++
- operating systems: UNIX(Solaris/..), Linux, MS-Window
- executables: pseudomarker, ilinkpseudo, makepedpseudo, mlinkpseudo, linkmappseudo, unknownpseudo
- reference: HHH Goring, JD Terwilliger (2000), "Linkage analysis in the presence of errors IV: joint pseudomarker analysis of linkage and/or linkage disequilibrium on a mixture of pedigrees and singletons when the mode of inheritance cannot be accurately specified", American Journal of Human Genetics, 66:1310-1327.
- PSEUDOMARKER.M
- full name:
- version: 2.03
- descriptions: PSEUDOMARKER is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses.
- authors: Saunak Sen, Gary Churhcill (Jackson Lab, email: pseudomarker@jax.org)
- web/ftp: http://www.jax.org/staff/churchill/labsite/software/pseudomarker/index.html
- source code language: MATLAB
- operating systems:
- executables:
- reference: Sen, Churchill (2001), "A statistical framework for quantitative trait mapping", Genetics, 159:371-387.
- PYPOP
- full name: PYthon for POPulation genetics
- version: beta 0.6 (April 2005)
- descriptions:
- authors: Alex Lancaster, Mark P Nelson, Richard M Single, Diogo Meyer, Glenys Thomson
- web/ftp: http://www.pypop.org/
- source code language: Python
- operating systems: MS-Windows(98/2000/XP), Linux
- executables:
- reference: Lancaster, Nelson, Single, Meyer, Thomson (2003), "PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data", Proceedings of the Pacific Symposium on Biocomputing, 8:514-525.
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