- MACH (see also MINIMAC )
- full name: MArkov Chain Haplotyper
- version: 1.0
- descriptions: MACH is a Markov Chain based haplotyper. It can be resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
- authors: Yun Li (email: ylwtx@umich.edu), Goncalo Abecasis (email: goncalo@umich.edu)
- web/ftp: http://www.sph.umich.edu/csg/abecasis/MACH/index.html
- source code language:
- operating systems:
- executables:
- reference:
- 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(5):771-789. [html]
- 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.
- MAOS
- full name: Meta-Analysis with Overlapping Subjects
- version:
- descriptions: Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. MAOS implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance.
- authors: Danyu Lin, Patrick Sullivan (Univ North Carolina)
- web/ftp: http://www.bios.unc.edu/~lin/software/MAOS/
- source code language: C++
- operating systems:
- executables:
- reference: Lin, Sullivan (2009), "Meta-analysis of genome-wide association studies with overlapping subjects", American Journal of Human Genetics, 85(6):862-872.
- 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.
- MAREYMAP
- full name:
- version:
- descriptions: MareyMap is a meiotic recombination rate estimation program.
- authors:
- web/ftp: http://pbil.univ-lyon1.fr/software/mareymap/
- source code language: R, tcl/tk
- operating systems:
- executables:
- reference: Rezvoy, Charif, Gueguen, Marais (2007), "MareyMap: an R-based tool with graphical interface for estimating recombination rate", Bioinformatics, 23:2188-2189.
- MARGARITA
- full name:
- version:
- descriptions: Margarita infers genealogies from population genotype data and uses these to map disease loci. These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events.
- authors: Richard Durbin (Wellcome Trust Sanger Institute)
- web/ftp: http://www.sanger.ac.uk/resources/software/margarita/
- source code language: Java
- operating systems:
- executables:
- reference:
- 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(2):336-354. [html]
- 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 (1987), Genomics,1,174-181.
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),
"Rapid multipoint linkage analysis of recessive traits in nuclear families, including homozygosity mapping",
American Journal of Human Genetics, 56(2):519-527.
[abstract]
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 (1987), Genomics,1,174-181.
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),
"Complete multipoint sib-pair analysis of qualitative and quantitative traits",
American Journal of Human Genetics, 57(2):439-454.
[abstract]
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 (2001), " Map Manager QTX, cross-platform software for genetic mapping", Mammalian Genome, 12(12):930-932.
- 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.
- MDR
- full name: Multifactor Dimensionality Reduction
- version: 2.0 beta 6
- descriptions: MDR is a data mining strategy for detecting and characterizing nonlinear interactions among discrete attributes (e.g. SNPs, smoking, gender, etc.) that are predictive of a discrete outcome (e.g. case-control status). The MDR software combines attribute selection, attribute construction and classification with cross-validation to provide a powerful approach to modeling interactions.
- authors: Jason Moore (email:jason.h.moore@dartmouth.edu)
- web/ftp: http://www.multifactordimensionalityreduction.org/
- source code language:
- operating systems:
- executables:
- reference:
Ritchie, Hahn, Roodi, Bailey, Dupont, Parl, Moore (2001),
"Multifactorial dimensionality reduction reveals high-order
interactions among estrogen metabolism genes in sporadic breat
cancer",
American Journal of Human Genetics, 69:138-147.
Moore, Gilbert, Tsai, Chiang, Holden, Barney, White (2006), "A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility", Journal of Theoretical Biology, 241:252-261.
- MDR-PDT
- full name: Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test
- version: beta
- descriptions:
- authors: ER Martin, MD Ritchie, L Hahn, S Kang, JH Moore
- web/ftp: http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=mdrpdt
- source code language:
- operating systems:
- executables:
- reference: Martin, Ritchie, Hahn, Kang, Moore (2006), "A novel method to identify gene-gene effects in nuclear families: the MDR-PDT", Genetic Epidemiology, 30:111-123.
- MECPM
- full name: Maximum Entropy Conditional Probability Moldeling
- version:
- descriptions:
- authors:
- web/ftp: http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm
- source code language:
- operating systems:
- executables:
- reference: Miller, Zhang, Yu, Liu, Chen, Langefeld, Herrington, Wang (2009), "An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions", Bioinformatics, to appear.
- 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
- MEGASNPHUNTER
- full name:
- version:
- descriptions: MegaSNPHunter takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome.
- authors:
- web/ftp: http://bioinformatics.ust.hk/MegaSNPHunter.html
- source code language:
- operating systems:
- executables:
- reference: Wan, Yang, Yang, Xue, Tang, Yu (2009), "MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions from whole genome data", BMC Bioinformatics, 10:13.
- MENDEL
- full name:
- version: 8.0.1 (expire April 2009)
- 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/
- source code language: FORTRAN77
- operating systems:
- executables:
- reference:
Lange, Weeks, Boehnke (1988),
Genetic Epidemiology, 5:471-471.
module USERM14: Stringham, Boehnke (1996), "Identifying marker typing incompatibilities in linkage analysis", American Journal of Human Genetics, 59(4):946-950. [abstract]
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", Frontiers in Artificial Intelligence and Applications, 163:29-37.
- 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.
- METAL
- full name: METa AnaLysis Helper
- version:
- descriptions: The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.
- authors: Goncalo Abecasis (email: goncalo@umich.edu)
- web/ftp: http://www.sph.umich.edu/csg/abecasis/Metal/
- source code language:
- operating systems:
- executables:
- reference:
- 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), "Model-free linkage analysis using likelihoods", American Journal of Human Genetics, 57(3):703-716. [abstract]
- 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),
"Multipoint analysis of human quantitative genetic variation",
American Journal of Human Genetics, 47(6): 957-967.
[abstract]
Goldgar, Oniki (1992), "Comparison of a multipoint identity-by-descent method with parametric multipoint linkage analysis for mapping quantitative traits", American Journal of Human Genetics, 50(3):598-606. [abstract]
online manual (from Wellcome Trust)
- MINIMAC (see also MACH )
- full name:
- version:
- descriptions: minimac is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, "mini", refers to the modest amount of computational resources it requires. The second, "mac", is short hand for MaCH, our widely used algorithm for genotype imputation.
- authors: Goncalo Abecasis, Christian Fuchsberger (Univ Michigan)
- web/ftp: http://genome.sph.umich.edu/wiki/Minimac
- source code language:
- operating systems:
- executables:
- reference:
- 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:
- MIXSCORE
- full name:
- version: 1.9 (March 2011)
- descriptions: MIXSCORE is a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations.
- authors: Alkes Price (Harvard Univ)
- web/ftp: http://www.hsph.harvard.edu/faculty/alkes-price/software/
- source code language:
- operating systems:
- executables:
- reference: Pasaniuc et al. (2011), "Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium", PLoS Genetics, 7:e1001371.
- 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), "Robustness and power of the maximum-likelihood-binomial and maximum-likelihood-score methods, in multipoint linkage analysis of affected-sibship data", American Journal of Human Genetics, 63(2):638-647. [abstract]
- 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 (1995), Genetica, 96:169-178.
- 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.
- MOSCPHASER
- full name: Mixture Of Cnv-Snp PHASER
- version:
- descriptions: inferring haplotypes composed of both CNV alleles and SNP alleles
- authors: Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda (email: tsunoda@src.riken.jp)
- web/ftp: http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip
- source code language:
- operating systems:
- executables:
- reference:
Kato, Nakamura, Tsunoda (2008),
"MOCSphaser: a haplotype inference tool from a mixture of
copy number variation and single nucleotide polymorphism data",
Bioinformatics, 24(14):1645-1646.
http://emu.src.riken.jp/MOCSphase/SuppInfor.doc
- 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 2.8.3 (March 2008)
- 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), "Minimum-recombinant haplotyping in pedigrees", American Journal of Human Genetics, 70(6):1434-1445. [html]
- 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/
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.
- MULTIQTL
- full name:
- version: 2.6
- descriptions: MultiQTL software integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data.
- authors: Efim Ronin, David Mester, Dina Minkov, Ori Orion, Abraham Korol
- web/ftp: http://www.multiqtl.com/
- source code language:
- operating systems:
- executables:
- reference:
- availability: contact: sales@multiqtl.com. tel: 972-4824-0449. FAX: 972-4824-6554. address: MultiQTL Ltd, Institute of Evolution, Haifa University, Haifa, Israel 31905
- 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.
- NUCULAR
- full name:
- version:
- descriptions: A program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers.
- authors: Mathieu Lemire (email: mlemire@sdf.lonestar.org)
- web/ftp: http://mlemire.freeshell.org/software.html
- source code language:
- operating systems:
- executables:
- reference: Lemire (2005), "A simple nonparametric multipoint procedure to test for linkage through mothers or fathers as well as imprinting effects in the presence of linkage", BMC Genetics, 6(Suppl 1):S159.
O - ONEMAP (see R/ONEMAP )
- OLORIN
- full name:
- version: October 2011
- descriptions: Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets.
- authors: James Morris, Jeffrey Barrett (Wellcome Trust Sanger Institute)
- web/ftp:
http://www.sanger.ac.uk/resources/software/olorin/
http://sourceforge.net/p/olorin/home/ - source code language: Java
- operating systems: any platform with Java 1.6 or later
- executables:
- reference:
- 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 (2004), "Ordered subset analysis in genetic linkage mapping of complex traits", Genetic Epidemiology, 27(1):53-63.
- 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 - P_ACT
- full name: P-values: Adjustment for Correlated Tests
- version: 1.2
- descriptions: P_ACT is an R program that adjusts sets of up to 1000 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests.
- authors:
- web/ftp: http://csg.sph.umich.edu/boehnke/p_act.php
- source code language:
- operating systems:
- executables:
- reference: Conneely, Boehnke (2007), "So many correlated tests, so little time! Rapid adjustment of p-values for multiple correlated tests", American Journal of Human Genetics, 81(6):1158-1168. [html]
- 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.
- PASS PEDIGREE
- full name:
- version:
- descriptions: PASS Pedigree is drawing the most complex family trees in a matter of minutes instead of hours of work. The basis of this is an algorithm for automatically builing a family tree. Of course, manual adjustments in the family tree can be made for your specific requirements. PASS Pedigree meets all international conventions concerning the drawing of pedigrees. A converter can convert historical Cyrillic pedigrees automatically to PASS Pedigree. Unlike before, all your family trees are stored in one single database. PASS Pedigree can intelligently connect to many genetic centers (e.g. three genetic centers in the Netherlands) with the existing patient information, via the lab system HELIX based on HL7 techniques.
- authors: PASS (Pro Active Software Solutions) Software
- web/ftp:
http://www.pass-software.com/Producten/PASSPedigree.aspx (in Dutch)
http://www.pass-software.com/Producten/PASSPedigree/tabid/113/language/en-US/Default.aspx (in English) - source code language:
- operating systems:
- executables:
- reference:
- availability: price
- PATH
- full name:
- version: 1.0.7 (September 28, 2009)
- descriptions: The Path web application is a first-step bioinformatics approach to investigate gene-gene interactions in genetic association studies. Path is designed to do: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables.
- authors: email: genapha@mrl.ubc.ca
- web/ftp: http://genapha.icapture.ubc.ca/PathTutorial/
- source code language:
- operating systems: MS-Windows, Linux
- executables:
- reference: Zamer, Tripp, Ellis, Daley (2009), "Path: a tool to facilitate pathway-based genetic association analysis", Bioinformatics, 25(18):2444-2446.
- 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: 3.6.1
- 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:
Lange, DeMeo, Silverman, Weiss, Laird (2003),
"Using the noninformative families in family-based
association tests: A powerful new testing strategy",
American Journal of Human Genetics, 73(4):801-811.
[html]
Lange, DeMeo, Silverman, Weiss, Laird (2004), "PBAT: tools for family-based association studies", American Journal of Human Genetics, 74(2):367-369. [html]
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(1):146-154. [html]
- 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". 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:
Bennet, Steinhaus, Uhrich, O'Sullivan, Resta, Lochner-Doyle, Markel, Vincent, Hamanishi(1995),
"Recommendations for standardized human pedigree nomenclature.
pedigree standardization task force of the national society of genetic counselors",
American Journal of Human Genetics, 56(3):745-752.
[abstract]
A Golla (1997), Medizinische Genetik, 4:595-597.
H Plendl (1998), Medizinische Genetik, 1:50-51. - 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),
"PedCheck: a program for identification of genotype incompatibilities in linkage analysis",
American Journal of Human Genetics, 63(1):259-266.
[abstract]
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:
- 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:
- 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.
- PEDPEEL
- full name:
- version:
- descriptions: The program prepares pedigree data for calculation of Elston-Stewarts' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays
- authors: Nadezhda Belonogova (email: adg101@mail.ru), Tatiana I. Axenovich
- web/ftp: http://mga.bionet.nsc.ru/soft/pedpeel/
- source code language:
- operating systems:
- executables:
- reference: Belonogova, Axenovich (2007), "Optimal peeling order for pedigrees with incomplete genotypic information", Computational Biology and Chemistry , 31(3):173-177.
- 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.
- 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.
- PEDSCRIPT
- full name:
- version: 2004 (not actively maintained)
- descriptions: PedScript is a tool that allows scripting of simple modifications to pedigree files.
- authors:
- web/ftp: http://genome.sph.umich.edu/wiki/PedScript
- source code language:
- operating systems:
- executables: anonymize, mendelcheck, nuke, trim, sample
- reference:
- 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.
- PEER
- full name:
- version:
- descriptions: PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. It can be used to detect eQTL.
- authors:
- web/ftp: http://www.sanger.ac.uk/resources/software/peer/
- source code language: C++
- operating systems:
- executables:
- reference: Stegle, Parts, Durbin, Winn (2010), "A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies", PLoS Computational Biology, 6:e1000770.
- 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/epidemiologie-krebserkrankungen/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.
- PLAYPUS
- full name:
- version:
- descriptions: an integrated variant caller
- authors: Gerton Lunter, Martin Goodson (Wellcome Trust Centre of Human Genetics, Oxford Univ)
- web/ftp: http://www.well.ox.ac.uk/platypus
- source code language:
- operating systems:
- executables:
- reference:
- 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), "Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms", American Journal of Human Genetics, (letter), 71(5):1242-1247-?. [html]
- PLINK (see also PLINK/SEQ )
- full name:
- version: 1.03
- 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, 81(3):559-575. [html]
- PLINK/SEQ (see also PLINK )
- full name:
- version:
- descriptions: PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs.
- authors:
- web/ftp: http://atgu.mgh.harvard.edu/plinkseq/
- source code language: C/C++, R
- operating systems: MacOS, Linux
- executables:
- reference:
- 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.
- POLYMUTT
- full name: POLYmorphism and de novo MUTaTion call in families with sequencing data
- version:
- descriptions: The program polymutt implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the [VCF] format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file.
- authors: B Li, G Abecasis (Univ Michigan)
- web/ftp: http://genome.sph.umich.edu/wiki/Polymutt:_a_tool_for_calling_polymorphism_and_de_novo_mutations_in_families_for_sequencing_data
- source code language:
- operating systems:
- executables:
- reference:
- POLYPHEN
- full name: POLYmorphism PHENotyping
- version:
- descriptions: PolyPhen-2 is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. It can be used in prioritize functional SNPs in a genetic study.
- authors:
- web/ftp:
http://genetics.bwh.harvard.edu/pph2/ (POLYPHEN-2)
http://genetics.bwh.harvard.edu/pph/ (POLYPHEN-1) - source code language:
- operating systems:
- executables:
- reference:
Sunyaev, Eisenhaber, Rodchenkov, Eisenhaber, Tumanyan, Kuznetsov (1999),
"PSIC: profile extraction from sequence alignments with position-specific
counts of independent observations",
Protein Engineering, 12:387-394.
Ramensky, Bork, Sunyaev (2002), "Human non-synonymous SNPs: server and survey", Nucleic Acids Research, 30:3894-3900.
Adzhubei, Schmidt, Peshkin, Ramensky, Gerasimova, Bork, Kondrashov, Sunyaev (2010), "A method and server for predicting damaging missense mutations", Nature Methods, 7:248-249.
- 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.homepages.ed.ac.uk/pmckeigu/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
http://cran.r-project.org/web/packages/popgen/index.html (removed from CRAN) - source code language: R
- operating systems:
- executables: popdiv, ps, nps, treesim, simMD
- reference:
- POWER