Sofwareslist

An Alphabetic List
of
Genetic Analysis
Software
PAGE 3 (M-P)
what's new | link to other sources | obsolete programs

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M
 MACH (see also MINIMAC )
o full name: MArkov Chain Haplotyper
o version: 1.0
o descriptions: MACH is a Markov Chain based haplotyper. It can be resolve long
haplotypes or infer missing genotypes in samples of unrelated individuals.
o authors: Yun Li (email: ylwtx@umich.edu), Goncalo Abecasis
(email: goncalo@umich.edu)
o web/ftp: http://www.sph.umich.edu/csg/abecasis/MACH/index.html
o source code language:
o operating systems:
o executables:
o reference:
 MADELINE
o full name:
o version: 0.935 (July 2004)
o 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.
o Authors: Edward Trager (email: ehtrager@umich.edu)
o web/ftp: http://eyegene.ophthy.med.umich.edu/
o source code language: C
o operating systems: UNIX (Solaris/FreeBSD/OpenBSD/MacOS), MS-Windows,
Cygwin, Linux,
o executables: madeline
o reference: http://eyegene.ophthy.med.umich.edu/madeline-0.935/
 MADMAPPER
o full name:
o version: September 2005
o 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/
o authors: Alexander Kozik (UC Davis Genome Center)
o web/ftp: http://www.atgc.org/XLinkage/MadMapper/
o source code language: Python
o executables: MadMapper_RECBIT, MadMapper_XDELTA
o reference:
 MAGIC
o full name: Marker And Gene Interpolation and Correlation
o version: 1.0
o descriptions:
o 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)
o web/ftp: http://cogent.iop.kcl.ac.uk/MaGIC.cogx
o source code language: Microsoft Visual Foxpro
o operating systems: MS-Windows (95/98/NT/2000/XP)
o executables:
o 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
o full name:
o version: 1.0 (Jan 2000)
o descriptions: complex segregaton analysis in animal pedigrees
o authors: Yurii Aulchenko (email: yurii@bionet.nsc.ru)
o web/ftp: http://mga.bionet.nsc.ru/soft/maia-1.0/
ooperating systems:
oexecutables:
oreference:
 MAKEPED
o full name: MAKE PEDfiles
o alias: LINKAGE/MAKEPED
o version:
o descriptions: part of the LINKAGE auxiliary program
o authors: Peter Cartwright (University of Utah, now Cimarron
Software pc@cimsoft.com )
o web/ftp: ftp://linkage.rockefeller.edu/software/linkage
o source code language: C and Pascal
o operating systems: UNIX, VMS, MS-DOS, OS2
o executables:
o reference:
 MALDSOFT
o full name:
o version: 1.0
o 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.
o authors: Giovanni Montana, Jonathan Pritchard
(email: jpritcha@genetics.uchicago.edu)
o web/ftp: http://pritch.bsd.uchicago.edu/software/maldsoft_download.html
o operating systems: UNIX, Linux, MS-Windows (DOS/Window...)
o executables:
o 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
o full name: Multivariate Association Mapping Algorithms
o version:
o descriptions:
o authors:
o web/ftp: http://polymorphism.ucsd.edu/cgi-bin/PRL/mama/mama.cgi
o operating systems: web-based
o executables:
o reference:
 MANTEL-STRUCT
o full name:
o version:
o descriptions: tests for population structure through the use of Mantel tests
o authors: Mark Miller (email: mark.miller@usu.edu)
o web/ftp: http://www.marksgeneticsoftware.net/
o operating systems: MS-Windows
o executables:
o reference: Miller (1999), "MANTEL-STRUCT: a program for the detection of
population structure via mantel tests", Journal of Heredity, 90:258-259.
 MAOS
ofull name: Meta-Analysis with Overlapping Subjects
oversion:
odescriptions: 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.
o authors: Danyu Lin, Patrick Sullivan (Univ North Carolina)
o web/ftp: http://www.bios.unc.edu/~lin/software/MAOS/
o source code language: C++
o executables:
o 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
o full name: (MAP+H is the radiation Hybrid module of MAP+)
o version:
o descriptions: multiple pairwise linkage analysis under interference
o authors: A Collins (email: arc@southampton.ac.uk ),
D. Shields,
NE Morton (University of Southampton, UK)
o 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
o source code language: FORTRAN
o operating systems: UNIX(SunOS/..)
o executables: map
o 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
ofull name: Windows software for the graphical presentation of linkage maps and
QTLs
o version: 2.2
o 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.
o Authors: Roeland E Voorrips (Plant Research International, Wageningen, The
Netherlands) (email: r.e.voorrips@plant.wag-ur.nl)
o web/ftp: http://www.biometris.wur.nl/uk/Software/MapChart/
o source code language: Delphi
o operating systems: MS-Windows (95/98/ME/NT4.0/2000)
o executables:
o 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
o full name:
o version: 4.0
o descriptions: create gene maps using either radiation hybrid data or linkage data
o authors: Wes Barris, Rachel Hawken
o web/ftp: http://www.wesbarris.com/mapcreator/
o source code language: Perl
o executables:
o reference:
o price: Postscript ($69 USD), Image ($69 USD), both ($99 USD)
 MAPDISTO
o full name:
o version: v1.7.0 (October 2007)
o 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.
o authors: Mathias Lorieux (m.lorieux@cgiar.org)
o web/ftp: http://mapdisto.free.fr/
o source code language: MS-Excel
o executables:
o reference:
 MAPDRAW
o full name:
o version: 2.2
o descriptions: MAPDRAW draws genetic linkage maps on PC same as what
MAPMAKER does on Mac.
o authors: Renhu Liu (email: liurenhu@21cn.com)
o web/ftp: http://www.nslij-genetics.org/soft/mapdraw.v2.2.xls
ftp://brassica.hzau.edu.cn
ftp://211.69.140.177
o source code language: Microsoft Visual Basic, Excel macro
o executables:
o 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 )
o full name:
o version: May 2002 (previously called MAPCOMP)
o 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
o Authors: Ralph van Berloo, Wageningen University, The Netherlands
(email: Ralph.vanberloo@pv.dpw.wau.nl)
o web/ftp: http://www.dpw.wau.nl/pv/PUB/MapComp/
o source code language: Delphi Pascal
o operating systems: MS-Window (32-bit)
o executables: MapComp.exe
o reference:
 MAPL
o full name: MAPping and QTL analysis
o version: March 2004
o 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.
o Authors: Ukai Tasuo, Ohsawa Ryo, Saito Akira, Hayashi Takeshi, Yasuo Ukai
(University of Tokyo, Japan) (email: tkawai@lbm.ab.a.u-tokyo.ac.jp)
o web/ftp: http://lbm.ab.a.u-tokyo.ac.jp/software.html
http://lbm.ab.a.u-tokyo.ac.jp/~ukai/mapl98.html
o source code language: Visual Basic (V5, professional)
ooperating systems: MS-Windows (95/98)
oexecutables:
oreference: 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
o full name:
o version:
o descriptions: MareyMap is a meiotic recombination rate estimation program.
o authors:
o web/ftp: http://pbil.univ-lyon1.fr/software/mareymap/
o source code language: R, tcl/tk
o executables:
o reference: Rezvoy, Charif, Gueguen, Marais (2007), "MareyMap: an R-based tool
with graphical interface for estimating recombination rate",Bioinformatics,
23:2188-2189.
 MARGARITA
o full name:
o version:
o 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.
o authors: Richard Durbin (Wellcome Trust Sanger Institute)
o web/ftp: http://www.sanger.ac.uk/resources/software/margarita/
o source code language: Java
o executables:
o reference:
 MATLINK
o full name:
o version:
o descriptions: A MATLAB utility for estimating genetic linkage in exotic line-
cross mating designs
o authors: J Clare Nelson (Kansas State University)
o web/ftp: http://coding.plantpath.ksu.edu/~jcn/MatLink.html
o source code language: MATLAB
o executables:
o reference:
 MDBLOCKS
o full name: Minimum Description length method for haplotype BLOCKS
o version:
odescriptions: Using the mimimum description length model to delineate
haplotype blocks
o authors: Eric C. Anderson and John Novembre (UC Berkeley)
o web/ftp: http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/
o executables:
o 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)
o full name:
o version: 3.0 (1992)
o descriptions:
o authors: Eric Lander, Phil Green, J. Abrahamson, A. Barlow, Mark Daly, Steve
Lincoln, L. Newburg (Whitehead Institute)
o web/ftp: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/
http://www-genome.wi.mit.edu/genome_software
o operating systems: UNIX, VMS, MS-DOS, MacOS
o executables: mapmaker
o reference: Lander et al (1987), Genomics,1,174-181.
online tutorial (version 3.0, 1987-1993)
 MAPMAKER/HOMOZ
o full name: homozygosity mapping
o version: May 1995
o descriptions: calculates multipoint lod scores in pedigrees with inbreeding loops
o 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 )
o web/ftp: ftp://ftp-genome.wi.mit.edu/distribution/software/homoz
o operating systems: UNIX
o executables:
o 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
o full name:
o version: new version in April 1995
o descriptions:
o authors: Eric Lander, Phil Green, J. Abrahamson, A. Barlow, Mark Daly, Steve
Lincoln, L. Newburg (Whitehead Institute)
o 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
o operating systems: UNIX, VMS, MS-DOS, MacOS
o executables:
o reference: Lander et al (1987), Genomics,1,174-181.
online tutorial and reference manual (v1.1, 1993)
 MAPMAKER/SIBS (see also GENEHUNTER)
o full name:
o version : 2.1 (Dec 1996)
o descriptions:
o 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)
o web/ftp: ftp://ftp-genome.wi.mit.edu/distribution/software/sibs
o executables: sibs
o 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
o full name:
o version : QTb29 (August 2000)
o descriptions: A graphic, interactive program to map quantitative trait loci by
regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait
mapping.
o authors: K.F. Manly
o web/ftp: http://www.mapmanager.org/mmQT.html
o source code language: Pascal
o operating systems: MacOS
o executables:
o reference: Manly and Olsen, Mammalian Genome, 10:327-334 (1999)
 MAP MANAGER QTX
o full name:
o version : QTXb20 (April 2004)
o 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.
o Authors: KF Manly, RH Cudmore, Jr., and JM Meer
o web/ftp: http://www.mapmanager.org/mmQTX.html
o source code language: C++ and cross-platform code from XVT
ooperating systems: MS-Windows, MacOS
oexecutables:
oreference: Manly, Cudmore, and Meer (2001), " Map Manager QTX, cross-
platform software for genetic mapping", Mammalian Genome, 12(12):930-932.
 MAPPOP
o full name:
o version: 1.0 (Jan 2000)
o descriptions: selects high resolution mapping subsamples and performs bin
mapping
o Authors: Dan Brown, Todd Vision (email: tjv@bio.unc.edu)
o web/ftp: http://www.bio.unc.edu/faculty/vision/lab/mappop/
o source code language: MatLab
o operating systems: UNIX, MS-Windows, MacOS, etc
o executables:
o 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
o full name: Software for the calculation of QTL positions on genetic maps
o version: 5 (October 2005)
o 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.
o authors: Johan W Van Ooijen, Martin P Boer, Ritsert C Jansen, Chris Maliepaard
(Plant Research International, Biometris, Wageningen, Netherlands)
(email: mapping@biometris.nl)
o web/ftp: http://www.mapqtl.nl
o source code language: ANSI C, Delphi
o operating systems: MS-Windows (95/98/ME/NT4.0/2000)
o executables:
o 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)
o full name: Monte Carlo Likelihood Estimation of Effective Population Size
o version: 1.1 (September 2001)
o descriptions:
o Authors: Eric Anderson (email: eriq@cqs.washington.edu , University of
Washington) and Ellen Williamson (University of California at Berkeley)
o web/ftp: http://www.stat.washington.edu/thompson/Genepi/pangaea.shtml
http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm
o operating systems: UNIX, MacOS
o executables:
o reference: Anderson, Williamson, Thompson (2000), "Monte Carlo evaluation of
the likelihood for Ne from temporally spaced samples", Genetics, 156:2109-2118.
 MCQTL
o full name: Multi-Cross QTL mapping
o version: v4.0
o 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.
o authors: Marie-Françoise Jourjon, Sylvain Jasson, Jacques Marcel, Baba Ngom,
Brigitte Mangin (email: brigitte.mangin@toulouse.inra.fr)
o web/ftp: http://carlit.toulouse.inra.fr/MCQTL/
o source code language: Java, C++
o operating systems: UNIX, Linux
o executables:
o reference: Jourjon, Jasson, Marcel, Ngom, Mangin (2005), "MCQTL: Multi-
allelic QTL mapping in multi-cross design", Bioinformatics, 21:128-130.
 MDR
o full name: Multifactor Dimensionality Reduction
o version: 2.0 beta 6
o 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.
o authors: Jason Moore (email:jason.h.moore@dartmouth.edu)
o web/ftp: http://www.multifactordimensionalityreduction.org/
o executables:
oreference: 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
o full name: Multifactor Dimensionality Reduction and genotype Pedigree
Disequilibrium Test
o version: beta
o descriptions:
o authors: ER Martin, MD Ritchie, L Hahn, S Kang, JH Moore
o web/ftp: http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=mdrpdt
o executables:
o 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
o full name: Maximum Entropy Conditional Probability Moldeling
o version:
o descriptions:
o authors:
o web/ftp: http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm
o executables:
o 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
o full name: a Manipulation Environment for Genetic Analyses
o version: 3.0 R9 (July 2006)
o 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).
o authors: Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P.
Mulvihill, Daniel E Weeks
oweb/ftp: http://watson.hgen.pitt.edu/register/
osource code language: C
ooperating systems: UNIX (Solaris, Silicon Graphics, OSF1, MacOS X), Linux,
MS-Windows, MacOS(X)
o executables: mega2
o 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
o full name:
o version:
o 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.
o authors:
o web/ftp: http://bioinformatics.ust.hk/MegaSNPHunter.html
o executables:
o 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
o full name:
o version: 8.0.1 (expire April 2009)
o 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.
o authors: Kenneth Lange (UCLA), Daniel Weeks (Pittsburgh), M. Boehnke
o web/ftp: http://www.genetics.ucla.edu/software/
o source code language: FORTRAN77
o executables:
o 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
o full name:
o version: 0.5b (July 2007)
o descriptions: Identifying all Mendelian inconsistencies in complex pedigree data
with thousand of individuals, including many loops and several errors. Can also
infer missing genotypes.
o 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
o web/ftp: http://www.inra.fr/mia/T/MendelSoft/
o operating systems: UNIX, Linux/Cygwin, MS-Windows, MacOS
o executables:
o 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
o full name: Multipoint Engine for Rapid Likelihood INference
o version: 1.0.1
o 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.
o Authors: Goncalo Abecasis (email: goncalo@umich.edu )
o web/ftp: http://www.sph.umich.edu/csg/abecasis/Merlin
http://www.sph.umich.edu/csg/abecasis/Merlin/download
o operating systems: UNIX. LINUX
o executables: merlin, pedstats, pedwipe
o 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
o full name: METa AnaLysis Helper
o version:
o 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.
o authors: Goncalo Abecasis (email: goncalo@umich.edu)
o web/ftp: http://www.sph.umich.edu/csg/abecasis/Metal/
o executables:
o reference:
 MFLINK
o full name: (nearly) model-free linkage analysis
o version:
o descriptions:
o authors: Dave Curtis, (email: dcurtis@hgmp.mrc.ac.uk) P.C. Sham
o web/ftp: http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html
ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/statgen/dcurtis/
o executables:
o reference: Curtis, Sham (1995), "Model-free linkage analysis using
likelihoods", American Journal of Human Genetics, 57(3):703-716. [abstract]
 MGA-MAPF2
o full name:
o version:
o descriptions: map QTLs in F-2 intercross in model organisms
o authors:
o web/ftp: http://mga.bionet.nsc.ru/soft/mgamapf2/
o operating systems: MS-DOS, MS-Windows (95/98/NT)
o executables:
o reference:
 MIDAS
o full name: Multiallelic Interallelic Disequilibrium Analysis Software
o version: 1.0
o descriptions: software for analysis and visualisation of interallelic disequilibrium
between multiallelic markers
o authors: Tom R Gaunt, Santiago Rodriguez, Carlos Zapata, Ian NM Day
o web/ftp: http://www.genes.org.uk/software/midas
http://www.sgel.humgen.soton.ac.uk/midas
o operating systems: MS-Windows(2000/XP), Linux, MacOS
o executables:
o reference: Gaunt, Rodriguez, Zapata, Day (2006), "MIDAS: software for analysis
and visualisation of interallelic disequilibrium between multiallelic
markers", BMC Bioinformatics, 7:227.
 MILD
o full name: MultIallelic Linkage Disequilibrium: a program for adjusted linkage
disequilibrium (LD) calculations
o version: 2.1 (2002)
o descriptions:
o authors: Yuril S Aulchenko (email: aulchenko@epib.fgg.eur.nl) (Erasmus
University Medical School, The Netherlands)
o web/ftp: http://www.geneticepi.com/Research/software/software.html
o operating systems: UNIX, Linux
o executables:
o reference:
 MIM
o full name: Multipoint Identical-by-descent Method
o version: 1.21 (March 1996)
o descriptions: multipoint IBD method for partitioning genetic variance of
quantitative traits to specific chromosome regions using data on nuclear families.
o authors: David Goldgar, Cathryn M. Lewis (Univ. Utah). contact person: Edward
Kort at edward@episun2.med.utah.edu
o web/ftp: ftp://morgan.med.utah.edu/pub/Mim
o executables:
o 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 )
o full name:
o version:
o 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.
o authors: Goncalo Abecasis, Christian Fuchsberger (Univ Michigan)
o web/ftp: http://genome.sph.umich.edu/wiki/Minimac
o executables:
o reference:
 MINSAGE
o full name: MINimal SAmple size for GEnotypes
o version:
o 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
o authors: Andreas Ziegler (email: koenigir@imbs.uni-luebeck.de)
o web/ftp: http://www.imbs.uni-luebeck.de/pub/minsage/index.html
o executables:
o reference: HG Gregorius (1980), "The probability of losing an allele when diploid
genotypes are sampled", Biometrics, 36:643-652.
 MITPENE
o full name:
o version:
o descriptions: A program for analysis of mitochondrial diseases
o authors:
o web/ftp: http://mga.bionet.nsc.ru/soft/mitpene/mitpene.html (in Russian)
o executables:
o reference:
 MIXSCORE
o full name:
o descriptions: MIXSCORE is a method for combining SNP association and
admixture association statistics to increase power in GWAS in admixed
populations.
o authors: Alkes Price (Harvard Univ)
o web/ftp: http://www.hsph.harvard.edu/faculty/alkes-price/software/
o executables:
o 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
o 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)
oversion:
odescriptions:
oAuthors: Michael Krawczak
oweb/ftp: http://www.uni-
kiel.de/medinfo/mitarbeiter/krawczak/download/index.html
o executables: asp, aspshare,easypat, mutprof,mutcomp,
findsire,patern,fingcomp,hapmax, mutpred
o reference:
 MMDRAWER
o full name:
o version: 0.2.0.0 (April 2003)
o 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.
o authors: Michael Brown
o web/ftp: http://www.emboss.co.nz/products.php?pid=2
o source code language: Delphi
o executables:
o reference:
 MLBGH
o full name: Maximum-Likelihood-Binomial analysis of affected sib-pair and
sibship data extended from the GENEHUNTER program
o version: 1.0
o descriptions: an extension of the GENEHUNTER program to perform sib-pair
and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB)
method.
o 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)
o web/ftp: ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)
http://genamics.com/software/downloads/mlbgh-1.0.tar.Z
o executables: mlbgh
o 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
o full name:
o version: Aug 1997
o 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.
o Authors: Dmitri Zaykin (email: zaykin@statgen.ncsu.edu)
o web/ftp: ftp://statgen.ncsu.edu/pub/zaykin/
o operating systems: UNIX, MS-Windows(95)
o executables: mld.x
o reference: Zaykin, Zhivotovsky, Weir (1995), Genetica, 96:169-178.
 MLR-TAGGING
o full name: Multivariate Linear Regression TAGGING
o version: 1.1
o descriptions: MLR-TAGGING can be used for tagging SNP selection and
genotype prediction
o authors: Alexander Zelikovsky (Georgia State Univ) (email: alexz@cs.gsu.edu),
Jingwu Jim He (email: jingwu@cs.gsu.edu)
o web/ftp: http://alla.cs.gsu.edu/~software/tagging/tagging.html
o executables:
o reference: He, Zelikovsky (2006), "MLR-tagging: informative SNP selection for
unphased genotypes based on multiple linear regression",Bioinformatics,
22(20):2558-2561.
 MOSCPHASER
o full name: Mixture Of Cnv-Snp PHASER
o version:
o descriptions: inferring haplotypes composed of both CNV alleles and SNP alleles
o authors: Mamoru Kato, Yusuke Nakamura, Tatsuhiko Tsunoda
(email: tsunoda@src.riken.jp)
o web/ftp: http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip
o executables:
o 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
o full name:
o version: 2.0
o 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
o authors: JP Gutierrez, LJ Royo, I Alvarez, F Goyache (Universidad Complutense
de Madrid, Spain)
o web/ftp: http://www.ucm.es/info/prodanim/html/JP_Web.htm
o executables:
o 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)
o full name: MOnte caRlo Genetic ANalysis
o version: version 2.8.3 (March 2008)
o 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)
o 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 .
o web/ftp: http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.sh
tml
o operating systems: UNIX (Compaq-Alpha, Solaris and others), Linux
o 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
o full name: Microarray Pooled DNA Analyser
o 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.
o 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
o web/ftp: http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm
o source code language: MATLABR
o operating systems: MS-Windows(Windows98/2000/XP)
o executables: mpda
o reference: Yang, Huang, Li, Lin, Yu, Diccianni, Wu, Chen, Fann (2008),
"MPDA: Microarray Pooled DNA Analyzer", BMC Bioinformatics, 9:196.
 MRH
ofull name: Minimum Recombinant Haplotype
oversion: 0.2 (May 2003)
odescriptions:
oAuthors: Dajun Qian (City of Hope National Medical Center,
email: dqian@coh.org)
o web/ftp: http://www-rcf.usc.edu/~gqian/software.htm (not available)
o operating systems: MS-Windows, UNIX(Solaris)
o executables:
o reference: Qian, Beckmann (2002), "Minimum-recombinant haplotyping in
pedigrees", American Journal of Human Genetics, 70(6):1434-1445. [html]
 MULTIDISEQ
o full name:
o version:
o descriptions: MULTIDISEQ is multipoint linkage analysis software which allows
Marker-Marker LD
o authors: Tero Hiekkalinna (email: tero.hiekkalinna@helsinki.fi)
o web/ftp: http://www.helsinki.fi/~tsjuntun/multidiseq/
o executables:
o 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
o full name:
o version:
o descriptions: program for automated construction of genetic maps
o authors: Tara Matise (email: matise@biology.rutgers.edu), Mark Perlin, Aravinda
Chakravarti
o web/ftp: http://compgen.rutgers.edu/Multimap/
http://compgen.rutgers.edu/multimap/multimapdist.html
osource code language: LISP
ooperating systems: UNIX (Sun/Compaq-Alpha/HP..)
oexecutables:
oreference: Matise,Perlin, Chakravarti, Nature Genetics, 6, 384-390 (1994);
 MULTIMAPPER
o full name:
o version:
o descriptions: Bayesian QTL mapping software for analysing backcross, double
haploid, and F2 data from designed crossing experiments of inbred lines
o authors: Mikko J Sillanpaa (mail: mjs@rolf.helsinki.fi)
o web/ftp: http://www.rni.helsinki.fi/~mjs/
o executables:
o 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
o full name:
o version: 1.1
o descriptions: Bayesian QTL mapping software for analysing backcross and F2
data from designed crossing experiments of outbred lines
o authors: Mikko J Sillanpaa (mail: mjs@rolf.helsinki.fi)
o web/ftp: http://www.rni.helsinki.fi/~mjs/
o executables:
o reference: Sillanpaa, Arjas (1999), "Bayesian mapping of multiple quantitative
trait loci from incomplete outbred offspring data", Genetics, 151:1605-1619.
 MULTIPOPTAGSELECT
o full name:
o version: 1.1
o 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.
o authors: Bryan N. Howie, Christopher S. Carlson, Mark J. Rieder, and Deborah
A. Nickerson (University of Washington)
o web/ftp: http://droog.gs.washington.edu/multiPopTagSelect.html
o executables: multiPopTagSelect.pl
o reference: Howie, Carlson, Rieder, Nickerson (2006), "Efficient selection of
tagging single-nucleotide polymorphisms in multiple populations", Human
Genetics, 120(1):58-68.
 MULTIQTL
o full name:
o version: 2.6
o 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.
o authors: Efim Ronin, David Mester, Dina Minkov, Ori Orion, Abraham Korol
o web/ftp: http://www.multiqtl.com/
o executables:
o reference:
o 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
o full name:
o version: 1.1
o descriptions: analyze the numbers of individuals that founded new populations
following a bottleneck or founding event
o authors: Mohamed Noor (email: noor@duke.edu)
o web/ftp: http://www.biology.duke.edu/noorlab/multsim.html
o operating systems: MS-DOS
o executables:
o reference: Noor, Pascual, Smith (2000), "Genetic variation in the spread of
Drosophila subobscura from a nonequilibrium population", Evolution, 54:696-
703.
 MUTAGENESYS
o full name:
o version:
o 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.
o authors: Julia Stoyanovich, Itsik Pe'er (Columbia University)
o web/ftp: http://magnet.c2b2.columbia.edu/mutagenesys/
o executables:
o reference: Stoyanovich, Pe'er (2008), "MutaGeneSys: estimating individual
disease susceptibility based on genome-wide SNP array data",Bioinformatics,
24(3):440-442.
N
 NOCOM
o full name:
o version: Aug 1992
o descriptions: estimate parameters for mixture of normal distributions
o Authors: Jurg Ott (Rockefeller University)
o web/ftp: ftp://linkage.rockefeller.edu/software/utilities
o operating systems: MS-DOS, OS2
o executables:
o reference: Ott (1979), "Detection of rare major genes in lipid levels", Human
Genetics, 51:79-91.
online user's guide
 NOPAR
o full name:
o version: Aug 1995
o descriptions: non-parametric linkage and association tests primarily for a
quantitative trait
o authors: A Collins (email: arc@southampton.ac.uk), NE Morton. (University of
Southampton, UK)
o web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/nopar
o operating systems: UNIX(SunOS)
o executables:
o reference: Collins,Morton (1995), Human Heredity, 45:311-318.
 NUCULAR
o full name:
o version:
o 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.
o authors: Mathieu Lemire (email: mlemire@sdf.lonestar.org)
o web/ftp: http://mlemire.freeshell.org/software.html
o executables:
o 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
o full name:
o version: October 2011
o 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.
o authors: James Morris, Jeffrey Barrett (Wellcome Trust Sanger Institute)
o web/ftp: http://www.sanger.ac.uk/resources/software/olorin/
http://sourceforge.net/p/olorin/home/
o operating systems: any platform with Java 1.6 or later
o executables:
o reference:
 OSA
o full name: Ordered Subset Analysis
o version: 2.1
o 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.
o authors: William Duren, Mike Boehnke, Elizabeth Hauser
o web/ftp: http://wwwchg.duhs.duke.edu/software/osa.html
o operating systems: UNIX(Solaris), Linux
o executables: osa2.0
o 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
o full name:
o version: 1.1
o 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).
o authors: Julio Bonis , Laura Ines Furlong Ferran Sanz (University of Pompeu
Fabra, Spain) (email: fsanz@imim.es)
o web/ftp: http://ibi.imim.es/osirisform.html
o executables:
o reference: Bonis, Furlong, Sanz (2006), "OSIRIS: a tool for retrieving literature
about sequence variants", Bioinformatics, 22(20):2567-2569.
P
 P_ACT
o full name: P-values: Adjustment for Correlated Tests
o version: 1.2
o 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.
o authors:
o web/ftp: http://csg.sph.umich.edu/boehnke/p_act.php
o executables:
o 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 )
o full name: Pedigree ANalysis for Genetics (And Epidemiological Attributes)
o version:
o descriptions: Collection of nine packages for genetic analysis;
the original four BOREL, HARDY, MORGAN and PEDPACK, plus INSEGT,
LOKI, MCLEEPS, PEDFIDDLER, and ECLIPSE
o Authors: many authors: see individual packages. managed by EA Thompson
(University of Washington, email: thompson@stat.washington.edu).
o source code language: C or C++
o operating systems: UNIX (Compaq, Solaris, and others), Linux
o executables:
o reference:
 PAP
o full name: Pedigree Analysis Package
o version: 6.0 (December 2006)
o 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
o 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)
o web/ftp: http://hasstedt.genetics.utah.edu/
o source code language: FORTRAN 77
o executables: preped, descstat, prepap,simul, papdr (with 8 options),gpe
o reference: manual (version 5, PDF) online manual (version 4) (from Wellcome
Trust)
 PARENTE
o full name:
o version: 1.2 (February 2003)
o descriptions: parentage inference using molecular data from diploid codominant
markers
o authors: Stephanie Blanc-Manel (email: stephanie.manel@ujf-grenoble.fr)
o web/ftp: http://www2.ujf-grenoble.fr/leca/membres/manel.html
o executables:
o reference: Cercueil, Bellemain, Manel (2002), "PARENTE: computer program
for parentage analysis", Journal of Heredity, 93:458-459.
 PASS PEDIGREE
o full name:
o version:
o 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.
o authors: PASS (Pro Active Software Solutions) Software
o 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)
o executables:
o reference:
o availability: price
 PATH
o full name:
o version: 1.0.7 (September 28, 2009)
o 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.
o authors: email: genapha@mrl.ubc.ca
o web/ftp: http://genapha.icapture.ubc.ca/PathTutorial/
o operating systems: MS-Windows, Linux
o executables:
o reference: Zamer, Tripp, Ellis, Daley (2009), "Path: a tool to facilitate pathway-
based genetic association analysis", Bioinformatics, 25(18):2444-2446.
 PAWE
o full name: Power for Association With Error
o version: Dec 2002
o descriptions: Power and sample size calculations for genetic case-control
association studies allowing for errors
o authors: Derek Gordon (email: gordon@linkage.rockefeller.edu), assisted by
Michael Nothnagel
o web/ftp: http://linkage.rockefeller.edu/pawe/
o executables:
o reference: Gordon, Finch, Nothnagel, Ott (2002), Human Heredity, 54:22-33.
 PAWE-3D
o full name: Power for Association With Error in 3D
o version:
o descriptions:
o authors: D Gordon, C Haynes, J Blumenfeld, SJ Finch
o web/ftp: http://linkage.rockefeller.edu/pawe3d/
o operating systems: web-based
o executables:
o 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 )
o full name: Power calculation of family-Based Association Tests
o version: 3.6.1
o descriptions: PBAT is an interactive software package that provides tools for the
design and the data analysis of family-based association studies.
o authors: Christoph Lange (email: clange@hsph.harvard.edu) (Harvard Univ).
o web/ftp: http://www.biostat.harvard.edu/~clange/default.htm
o executables:
o 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
o full name: Pooled DNA Analyzer
o version:
o descriptions: a tool for analyses of pooled DNA data
o authors: Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann
(Institute of Biomedical Sciences, Academia Sinica, Taiwan)
o web/ftp: http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm
o executables:
o reference: Yang, Pan, Lin, Fann (2006), "PDA: pooled DNA analyzer", BMC
Bioinformatics, 7:233.
 PDPSYS
o full name: Pedigree Data Processing SYStem
o version: 1.0 (November 1998)
o descriptions: PDPSys is a Windows-based system designed for pedigree data
management, providing a graphical interface for pedigree construction and output.
o Authors: Fil Quiaoit (Fred Hutchinson Cancer Research Center,
email: fquiaoit@fhcrc.org)
o web/ftp: http://cougar.fhcrc.org/software.php
o source code language: Visual Basic, MS-Access
o operating systems: MS-Windows (95)
o executables: pdpsys
o reference:
 PDT
o full name: pedigree disequilibrium test
o version: 5.1
o 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.
o Authors: Eden Martin (Duke Univ)
o web/ftp: http://www.chg.duke.edu/software/pdt.html
o operating systems: UNIX(Solaris)
o executables:
o reference: Martin, Monks, Warren, Kaplan (2000), American Journal of Human
Genetics, 67(1):146-154. [html]
 PED
ofull name: PEdigree Drawing software
oversion: 5.1.0 (October 2006)
odescriptions: 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.
o Authors: Hansjoerg Plendl (email: plendl@medgen.uni-kiel.de )
o web/ftp: http://www.medgen.de/index.html
http://www.medgen.de/ped/index.htm
o source code language: Visual Smalltalk
o operating systems: MS-Windows (95/98/NT)
o executables: ped.exe
o 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.
o price: site license US$99.
 PEDAGREE
o full name: 1.00 (February 2002)
o version:
o descriptions: a program for detecting autosomal marker Mendelian
incompatibilities in pedigree data
o authors: Christine Couillault (email: kristin.c@free.fr)
o web/ftp: http://pedagree.free.fr/
o source code language: C, C++
o operating systems: UNIX, Linux, MS-Windows, MS-DOS,
o executables: pedagree
o reference:
 PEDCHECK
o full name:
o descriptions: identifying all Mendelian inconsistencies in pedigree data.
o Authors: J. R. O'Connell (email: jeff@sherlock.hgen.pitt.edu )
o web/ftp: http://watson.hgen.pitt.edu/register
o source code language: C, C++
o operating systems: UNIX(SunOS/Solaris/Compaq-Alpha/SGI-IRIX/..)
o executables:
o 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)
o full name:
o version: 0.5 (August 2005)
o 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.
o 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).
o web/ftp: http://www.stat.washington.edu/thompson/Genepi/Pedfiddler.shtml
o source code language: C,C++
o operating systems: UNIX (OSF1, and Solaris 2.7, AlphaLinux) MS-Windows
(XP Home/Win32/Win95), Linux
o executables:
o reference:
 PEDHUNTER
o full name:
o version:
o descriptions: a software package that facilitates creation and verification of
pedigrees within large genealogies.
o Authors: Agarwala, Biesecker, Hopkins, Francomano, Schffer (NIH)
o web/ftp: http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html
o executables:
o 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
o full name:
o version: 2.3
o descriptions: A pedigree visualization program specifically designed to draw
large, complex pedigrees.
o authors: John Garbe (University of Minnesota, email: jgarbe@umn.edu), Yang
Da (University of Minnesota, email: yda@umn.edu)
o web/ftp: http://animalgene.umn.edu/pedigraph/
o executables: pedigraph
o reference: J Garbe, Y Da (2003), Pedigraph user manual Version 1.1. Department
of Animal Science, University of Minnesota.
 PEDIGREE/DRAW
o full name:
o version: 6
o descriptions: pedigree drawing
o authors: Bennett Dyke (email: bdyke@darwin.sfbr.org ), Paul Mamelka (contact
person, email: paul@darwin.sfbr.org ), J. MacCleur, Southwest Foundation for
Biomedical Research
o web/ftp: http://www.pedigree-draw.com/
ftp://www.sfbr.org/pub/pedmgt/peddrw
o operating systems: MacOS
o executables:PedDraw
o reference: Am Soc Hum Genet annual meeting 1987 (Dyke, Mamelka, Am J.
Hum Genet, suppl 41, A253 (1987))
o price: disk and user's guide: US$45; user's guide: US$20; upgrade for disk:
US$15;
 PEDIGREEQUERY
o full name:
o version:
o descriptions: allows drawing pedigrees with a difficult structure, those containing
consanguinity loops, and those individuals with multiple mates or several related
families
o authors: A Kirichenko
o web/ftp: http://mga.bionet.nsc.ru/soft/index.html
http://mga.bionet.nsc.ru/PedigreeQuery/PedigreeQuery.html (in Russian)
o executables:
o reference: A Kirichenko (2003), "PedigreeQuery - software for pedigree drawing"
(abstract), American Journal of Human Genetics, suppl
 PEDIGREE-VISUALIZER
o full name:
o version:
o descriptions:
o authors: Limsoon Wong (National University of Singapore, Singapore)
o web/ftp: http://research.i2r.a-star.edu.sg:8080/kleisli/demos/pedigree/
o executables:
o reference:
 PEDJAVA
o full name: PedJava
o version: 1.1
o 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.
o Authors: Matthias Wjst (email: wjst@gsf.de), Juergen Knauth
(email: woodoo@bigfoot.de )
o web/ftp: http://cooke.gsf.de/wjst/download.cfm
o source code language: JDK
o operating systems: no restriction for client, server WIN 95/NT
o executables: pedJava, pedJavaServer
o reference: in preparation
 PEDMANAGER
o full name:
o alias: MAPMAKER/PEDMANAGER
o version: 0.9 (1997)
o descriptions:
o authors: Mary Pat Daly (previously Mary Pat Reeve) (MIT/Whitehead)
o web/ftp: http://www-genome.wi.mit.edu/ftp/distribution/software/pedmanager/
o executables: pedprep
o reference:
 PEDPACK (see also PANGAEA)
o full name:
o version: Version 2.2, July 1996
o descriptions: Programs for pedigree analysis, including segregation analysis, gene
extinction, and pedigree graphics.
o 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)
o operating systems: UNIX(Compaq-Alpha/..)
o executables:
o 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
o full name:
o version:
o 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
o authors: Nadezhda Belonogova (email: adg101@mail.ru), Tatiana I. Axenovich
o web/ftp: http://mga.bionet.nsc.ru/soft/pedpeel/
o executables:
o reference: Belonogova, Axenovich (2007), "Optimal peeling order for pedigrees
with incomplete genotypic information", Computational Biology and Chemistry ,
31(3):173-177.
 PEDPHASE
o full name:
o version: 2.0
o descriptions: inferring haplotypes from genotypes on pedigree data
o authors: Jing Li(email: jingli@eecs.cwru.edu)
o web/ftp: http://vorlon.case.edu/~jxl175/haplotyping.html
o executables:
o 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
o full name:
o version:
o descriptions: Pedigree Plotting Program for the Pedfile Format
o Authors: JE Stajich (email: jason@chg.mc.duke.edu), C Haynes
(email: carol@chgd.mc.duke.edu), MA Pericak-Vance (Duke University Medical
Center)
o web/ftp: http://www.chg.duke.edu/software/pedplot.html
o source code language: C++, Postscript
o operating systems: UNIX(Sparc-Solaris 2.5/DEC UNIX 4.0/x86-Solaris 2.6)
o executables: pedplot
o reference: Am Soc Hum Genet annual meeting 1998 (Stajich, Haynes, Pericak-
Vance, Am J Hum Genet, suppl, 63,A242).
 PEDRAW/WPEDRAW
o full name: Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-
Window version of PEDRAW)
o version: 2.5
o descriptions: a pedigree drawing program using LINKAGE data files
o authors: Dave Curtis (email: dcurtis@hgmp.mrc.ac.uk)
ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/statgen/dcurtis/
o operating systems: MS-DOS, MS-Windows, X-window
o executables:
o reference: Curtis (1990), Annals of Human Genetics, 54:365-367.
 PEDSCRIPT
o full name:
o version: 2004 (not actively maintained)
o descriptions: PedScript is a tool that allows scripting of simple modifications to
pedigree files.
o authors:
o web/ftp: http://genome.sph.umich.edu/wiki/PedScript
o executables: anonymize, mendelcheck, nuke, trim, sample
o reference:
 PEDSTATS
o full name:
o version: 0.6.8
o 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.
o authors: Janis Wigginton (email: wiggie@umich.edu), Goncalo Abecasis
(email: goncalo@umich.edu)
o web/ftp: http://www.sph.umich.edu/csg/abecasis/Pedstats/
o operating systems: Linux, UNIX, MS-Windows
o executables: pedstats
o reference: Wigginton, Abecasis (2005), "PEDSTATS: descriptive statistics,
graphics and quality assessment for gene mapping data", Bioinformatics,
21:3445-3447.
 PEDSYS
o full name:
o version: 2.0
o descriptions: a full-scale database system developed as a specialized tool for
management of genetic, pedigree and demographic data.
o authors: Bennett Dyke (email: bdyke@darwin.sfbr.org ), Paul Mamelka
(email: paul@darwin.sfbr.org ),
o web/ftp: http://www.sfbr.org/sfbr/public/software/pedsys/pedsys.html
ftp://www.sfbr.org/pub/pedmgt/pedsys
o operating systems: UNIX(SunOS,Solaris), MS-DOS, MacOS
o executables:
o reference:
o 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
o full name: PEDigree VIsualiZation API
o 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.
o authors: Christain Fuchsberger (email: christian.fuchsberger@eurac.edu), Mario
Falchi, Lukas Forer, Peter Pramstaller
o web/ftp: http://www.pedvizapi.org/
o source code language: Java, R
o executables:
o reference: Fuchsberger, Falchi, Forer, Pramstaller (2007), "PedVizApi: A Java
API for the interactive, visual analysis of extended pedigrees",Bioinformatics,
24(2):279-281.
 PEER
o full name:
o version:
o 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.
o authors:
o web/ftp: http://www.sanger.ac.uk/resources/software/peer/
o executables:
o 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
o full name: Pedigree Editor for LInkage Computer ANalysis
o version:
o descriptions: It is a utility for graphically editing the pedigree data files used by
programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN.
o authors: Frank Dudbridge (MRC, email: frank.dudbridge@mrc-bsu.cam.ac.uk )
o web/ftp: http://www.mrc-bsu.cam.ac.uk/personal/frank/software/pelican/
o executables:
o reference: F Dudbridge, T Carver, GW Williams (2004), "Pelican: pedigree editor
for linkage computer analysis", Bioinformatics, 20(14):2327-2328.
 PHASE
o full name:
o version: 2.0 (Sept 2003)
o 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.
o Authors: Matthew Stephens (email: stephens@stat.washington.edu)
o web/ftp: http://www.stat.washington.edu/stephens/software.html
previous site: http://www.stats.ox.ac.uk/mathgen/software.html
o executables:
o reference: Stephens, Smith, Donnelly (2001), AJHG, 68:978-989.
 PIAGE
o full name: Power of Indirect Association Studies of Gene-Environment
Interactions
o 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.
o authors: Rebecca Hein (email:r.hein@dkfz-heidelberg.de), Lars Beckmann
(email:l.beckmann@dkfz-heidelberg.de)
o web/ftp: http://www.dkfz.de/en/epidemiologie-
krebserkrankungen/software/software.html
o source code language: R
o executables:
o 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
o full name: PLAnt Breeding QTL analysis
o version:
o descriptions:
o authors: HF Utz (email: utzf@uni-hohenheim.de)
o web/ftp: https://www.uni-hohenheim.de/plantbreeding/software/
o executables:
o reference: Utz, Melchinger (1996), "PLABQTL: A program for composite
interval mapping of QTL", JAG
 PLABSIM
o full name: PLAnt Breeding SIMulation
o version: 1.0.1 (June 2005)
o descriptions:
o authors: Matthias Frisch (email: frisch@uni-hohenheim.de)
o web/ftp: http://www.uni-hohenheim.de/~frisch/software.html
o operating systems: UNIX(AIX), Linux, MS-Windows(NT)
o executables:
o reference: Frisch, Bohn, Melchinger (2000), "PLABSIM: software for simulation
of marker-assisted backcrossing", Journal of Heredity, 91:86-87.
 PLAYPUS
o full name:
o version:
o descriptions: an integrated variant caller
o authors: Gerton Lunter, Martin Goodson (Wellcome Trust Centre of Human
Genetics, Oxford Univ)
o web/ftp: http://www.well.ox.ac.uk/platypus
o executables:
o reference:
 PL-EM
o full name: Partition-Ligation EM algorithm for haplotype inference with single
nucleotide polymorphisms
o version:
o descriptions:
o authors: Jun Liu, Steve Qin, Tianhua Niu (Harvard Univ)
o web/ftp: http://www.people.fas.harvard.edu/~junliu/plem/
o executables:
o 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 )
o full name:
o version: 1.03
o descriptions: a whole-genome association analysis toolset
o authors: Shaun Purcell
o web/ftp: http://pngu.mgh.harvard.edu/purcell/plink/
o executables:
o 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 )
o full name:
o version:
o 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.
o authors:
o web/ftp: http://atgu.mgh.harvard.edu/plinkseq/
o source code language: C/C++, R
o operating systems: MacOS, Linux
o executables:
o reference:
 POINTER
o full name:
o version:
o descriptions: for complex segregation analysis with the mixed model (major locus
and polygenes).
o authors: NE Morton (University of Southampton, UK), D.C. Rao, J-M. Lalouel
o web/ftp: http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/pointer
o source code language: SUN FORTRAN (especially, the command "fsplit" is
needed)
o operating systems: UNIX (SunOS/..)
o executables:
o reference: Morton, Rao, Lalouel, "Methods in Genetic Epidemiology" (Karger,
1983).
 POLYMORPHISM
o full name:
o version: 1.4 (June 1999)
o descriptions: calculating the heterozygosity, PIC, and LIC values for polymorphic
markers
o Authors: Tianhua Niu, Sc.D. (Harvard Medical School,
email: tniu@hohp.harvard.edu)
o web/ftp:
o executables: powerlic
o 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
o full name: POLYmorphism and de novo MUTaTion call in families with
sequencing data
o version:
o 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.
o authors: B Li, G Abecasis (Univ Michigan)
o web/ftp: http://genome.sph.umich.edu/wiki/Polymutt:_a_tool_for_calling_polymo
rphism_and_de_novo_mutations_in_families_for_sequencing_data
o executables:
o reference:
 POLYPHEN
o full name: POLYmorphism PHENotyping
o version:
o 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.
o authors:
o web/ftp: http://genetics.bwh.harvard.edu/pph2/ (POLYPHEN-2)
http://genetics.bwh.harvard.edu/pph/ (POLYPHEN-1)
o executables:
o 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
o full name:
o version:
o descriptions: a program for analysis of case-control genetic association studies
using allele frequency measurements on DNA pools
o authors: Paul McKeiger (email: paul.mckeigue@ucd.ie) (University College
Dublin, Ireland)
o web/ftp: http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm
o executables: poolscore.R
o reference:
 POOL_STR
o full name: POOLing alleles of Short Tandem Repeat markers
o version: 1.1
o descriptions:
o authors: Yurii Aulchenko, Aida Bertoli-Avella, Cornelia van Duijn (Erasmus
University Medical School, The Netherlands)
o web/ftp: http://www.geneticepi.com/Research/software/software.html
http://www.geneticepi.com/Research/software/pool_str-1.1.tar.gz
o executables:
o 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
o full name:
o version: 1.1.2
o descriptions: POPDIST calculates a number of different genetic identities,
phylogeny reconstructing measures, and distance reconstructing measures
o authors: Bernt Guldbrandtsen (email: bg@genetics.agrsci.dk)
o web/ftp: http://genetics.agrsci.dk/~bg/popgen/
o operating systems: UNIX (AIX/IRIX/DECalpha), Linux, MacOS, MS-DOS, MS-
Windows(95)
o executables:
o 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
o full name:
o version:
o 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.
o authors: Jonathan Marchini (email: marchini@stats.ox.ac.uk)
o 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)
o executables: popdiv, ps, nps, treesim, simMD
o reference:
 POWER
o full name:
o version: 3.0
o 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).
o authors:
o web/ftp: http://dceg.cancer.gov/POWER/
o operating systems: MS-Window
o executables:
o 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
o full name:
o version: 3.25 (February 2006)
o 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.
o authors: Jack Liu
o web/ftp: http://statgen.ncsu.edu/powermarker/
o executables:
o reference: Liu, Muse (2005), "PowerMarker: an integrated analysis environment
for genetic marker analysis", Bioinformatics, 21(9):2128-2129.
 POWERTRIM
o full name:
o version:
o descriptions: automate the decision to remove objects from a pedigree with a
minimum loss information
o authors: Tricia Thornton, Jonathan Haines (Venderbilt University Medical
Center)
o web/ftp: http://phg.mc.vanderbilt.edu/content/powertrim
o executables:
o reference: Thornton, Haines (2003), "PowerTrim: an automated decision support
algorithm for preprocessing family-based genetic data", American Journal of
Human Genetics, 72(5):1280-1281. [html]
 POWQ
o full name:
o version:
o descriptions: A user-friendly, graphical package for power evaluation and
enhancement planning through variance component linkage analysis in a
multipoint framework.
o authors: Mario Falchi (email: mario.falchi@kcl.ac.uk) Cesare Cappio Borlino
o web/ftp: http://www.twin-research.ac.uk/WebPowQ/PowQ.htm
o executables:
o 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
o full name:
o version:
o descriptions: Excel spreadsheet to calculate power of affected sibpairs and TDT
analyses
o authors: Dave Curtis
o executables:
o reference:
 PREPLINK
o full name: MAKE PEDfiles
o alias: LINKAGE/PREPLINK
o version:
o descriptions: part of the LINKAGE auxiliary program
o authors: Peter Cartwright (University of Utah, now Cimarron
Software pc@cimsoft.com )
o web/ftp: ftp://linkage.rockefeller.edu/software/linkage or
o source code language: C and Pascal
o operating systems: UNIX, VMS, MS-DOS, OS2
o executables:
o reference:
 PREST
o full name: Pedigree RElationship Statistical Test
o version: 3.0.2 (February 2005)
o 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.
o authors: Lei Sun, Kenneth Wilder, Mary Sara McPeek (University of Chicago)
o web/ftp: http://fisher.utstat.toronto.edu/sun/Software/Prest or
previously, http://galton.uchicago.edu/~mcpeek/software/prest
o operating systems: Linux, UNIX(Solaris/..)
o executables: prest.solaris, prest.linux, altertest.solaris, altertest.linux
o reference: McPeek, Sun (2000), "Statistical tests for detection of misspecified
relationships by use of genome-screen data", American Journal of Human
Genetics, 66(3):1076-1094. [html]
 PRESTO
o full name:
o version: 1.0.1 (October 2007)
o descriptions: PRESTO performs permutation testing and computes empirical
distributions of order statistics for one and two stage association studies with
stratified or unstratified data.
o authors: Brian L Browning (email: b.browning@auckland.ac.nz)
o web/ftp: http://faculty.washington.edu/browning/presto/presto.html
o operating systems: MS-Windows, UNIX (Solaris/..), Linux, MacOS
o executables:
o reference: Browning (2008), "PRESTO: Rapid calculation of order statistic
distributions and multiple-testing adjusted P-values via permutation for one and
two-stage genetic association studies", BMC Bioinformatics, 9:309.
 PROBMAX
o full name:
o version:
o descriptions: assigning unknown parentage in pedigree analysis from known
genotypic pools of parents and progeny
o authors: Roy Danzmann (email: rdanzman@uoguelph.ca)
o web/ftp: http://www.uoguelph.ca/~rdanzman/software/PROBMAX/
o executables:
o 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.
 PROC QTL
o full name:
o version: 1.0 (January 2009)
o descriptions: PROC QTL is a user defined SAS procedure for mapping
quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure,
users need to obtain a copy of the executable file of PROC QTL and install the
software in their personal computers before PROC QTL can be executed. Of
course, users need a regular SAS license prior to the installation of PROC QTL.
Once PROC QTL is installed, it can be called just like any other SAS procedures.
Users will not notice the differences between this customized procedure and other
built-in SAS procedures.
o authors: Zhiqiu Hu (email: zhiqiu.hu@ucr.edu), Shizhong Xu
(shizhong.xu@ucr.edu)
o web/ftp: http://www.statgen.ucr.edu/software.html
o executables:
o reference: Hu and Xu (2009), "PROC QTL - A SAS procedure for mapping
Quantitative Trait Loci", Plant and Animal Genomes XVII Conference. January
10-14, 2009, San Diego, California (http://www.intl-
pag.org/17/abstracts/C02_PAGXVII_854.html ).
 PROFILER
o full name:
o version:
o 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.
o authors: Jeff O'Connell
o web/ftp: http://www.molecular-haplotype.org/profiler/profiler_intro.htm
o operating systems: Linux, UNIX(Solaris)
o executables:
o reference:
 PROGENY
o full name: Progeny Software, LLC
o version: 6.8 (December 2006)
o 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.
o authors: David Deram (Progeny Software, LLC)
o web/ftp: http://www.progenygenetics.com/
o source code language: C++ and Active X Controls
o operating systems: MS-Windows (95/98/2000/ME/NT/XP)
o executables:
o reference:
 PRT
o full name: Pedigree Reconstruction Tools
o version: 1.2
o descriptions: Partition of single generation into sibling groups
o authors: Anthony Almudevar (Dept Biostatistics and Computational Biology,
University of Rochester Medical Center,
email:anthony_almudevar@urmc.rochester.edu)
o web/ftp: http://www.urmc.rochester.edu/smd/biostat/Projects/Help/PC/Software_
Listings.htm
o executables: msg_proj
o 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.
 PSAT
o full name: Population Stratification Association Test
o version:
o descriptions:
o authors: G Kimmel, MI Jordan, E Halperin, R Shamir, RM Karp
o web/ftp: http://acgt.cs.tau.ac.il/psat/
o executables:
o reference: Kimmel, Jordan, Halperin, Shamir, Karp (2007), "A randomization test
for controlling population stratification in whole-genome association
studies", American Journal of Human Genetics, 81(5):895-905. [html]
 PSEUDO
o full name:
o version: 0.3.5
o 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.
o authors: Janis Wigginton (email:wiggie@umich.edu) and Goncalo Abecasis
o web/ftp: http://www.sph.umich.edu/csg/abecasis/pseudo/download
o operating systems: Linux, UNIX, MacOS, MS-Windows
o executables: pseudo, scan
o 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
o full name:
o version: 1.0.6b (November 2011)
o descriptions: PSEUDOMARKER is a linkage analysis software for joint linkage
and/or linkage disequilibrium analysis. PSEUDOMARKER can analyze different
data structures jointly such as cases-controls, trios, sib-pairs, sib-ships, and
extended families.
o Authors: Tero Hiekkalinna (email: tero.hiekkalinna@helsinki.fi), Joseph D
Terwilliger, Petri Norrgrann
o web/ftp: http://www.helsinki.fi/~tsjuntun/pseudomarker/
o source code language: C/C++
o operating systems: Linux
o executables: pseudomarker, ilinkpseudo, makepedpseudo, mlinkpseudo,
linkmappseudo, unknownpseudo
o reference: Goring, 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(4):1310-1327.
[html]
Hiekkalinna, Schäffer, Lambert, Norrgrann, Göring, Terwilliger (2011),
"PSEUDOMARKER: a powerful program for joint linkage and/or linkage
disequilibrium analysis on mixtures of singletons and related individuals", Human
Heredity, 71:256-266.
[abstract]
 PSEUDOMARKER.M
o full name:
o version: 2.03
o descriptions: PSEUDOMARKER is a set of programs written in MATLAB for
the analysis of QTL data from inbred line crosses.
o authors: Saunak Sen, Gary Churhcill (Jackson Lab,
email: pseudomarker@jax.org)
o web/ftp: http://www.jax.org/staff/churchill/labsite/software/pseudomarker/index.h
tml
o source code language: MATLAB
o executables:
o reference: Sen, Churchill (2001), "A statistical framework for quantitative trait
mapping", Genetics, 159:371-387.
 PYPOP
o full name: PYthon for POPulation genetics
o version: beta 0.7.0 (September 2008)
o descriptions:
o authors: Alex Lancaster, Mark P Nelson, Richard M Single, Diogo Meyer,
Glenys Thomson
o web/ftp: http://www.pypop.org/
o operating systems: MS-Windows(98/2000/XP), Linux
o executables:
o 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.
Lancaster, Single, Solberg, Nelson, Thomson (2007), "PyPop update - a software
pipeline for large-scale multilocus population genomics", Tissue Antigens,
69(s1):192-197.
genetic analysis software list: www.nslij-genetics.org/ga/soft (page 3)

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