Resource Name

Genetic Analysis Software

RRID:SCR_013155 RRID Copied

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Genetic Analysis Software (RRID:SCR_013155)

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URL: http://www.jurgott.org/linkage/ListSoftware.html

Proper Citation: Genetic Analysis Software (RRID:SCR_013155)

Description: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs.

Abbreviations: GAS

Synonyms: An Alphabetic List of Genetic Analysis Software

Resource Type: software resource, database, data or information resource, catalog, data set

Keywords: gene mapping, gene, genetic, genomic, model, modeling, software program, genetic linkage analysis, qtl analysis, genetic marker order, genetic association analysis, haplotype construction, pedigree drawing, population genetics

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Funding:

Availability: THIS RESOURCE IS NO LONGER IN SERVICE

Resource Name: Genetic Analysis Software

Resource ID: SCR_013155

Alternate IDs: nif-0000-33506

Alternate URLs: http://lab.rockefeller.edu/ott/geneticsoftware

Old URLs: http://linkage.rockefeller.edu/soft/

Record Creation Time: 2022-01-29 12:03:14

Record Last Update: 2025-03-29 11:13:00

This resource

is used by	NIF Data Federation
lists	EM-DECODER
lists	ENTROPY BLOCKER
lists	SOAP
lists	ADEGENET
lists	2LD
lists	SQTL
lists	POLYMORPHISM
lists	EDAC
lists	FEST
lists	GENEHUNTER SAD
lists	COMDS
lists	CHAPLIN
lists	CRIMAP
lists	DCHIP LINKAGE
lists	FLOSS
lists	HAP 1
lists	HAPSCOPE
lists	LDB/LDB+
lists	LOCUSMAP
lists	MRH
lists	PEDIGREE-VISUALIZER
lists	PEDPHASE
lists	QTL CAFE
lists	RHMAPPER
lists	R/GC, R/GCF
lists	R/GWAPOWER
lists	R/WEIGHTED FDR
lists	SIMM
lists	SOLAR
lists	TDTHAP
lists	HWESTRATA
lists	TDT-PC
lists	EQTL EXPLORER
lists	GAS2
lists	LDMET
lists	LAMBDAA
lists	EIGENSOFT/EIGENSTRAT
lists	Happy
lists	LAMP
lists	CLUSTAG
lists	OSA
lists	SIMIBD
lists	SNPSTATS
lists	Haploview
lists	QGene
lists	PAWE-3D
lists	MILD
lists	PEDPLOT
lists	GS-EM
lists	PEDSCRIPT
lists	Multipoint Identical-by-descent Method
lists	PARENTE
lists	Integrated Software
lists	PEDRAW/WPEDRAW
lists	POPDIST
lists	TDTASP
lists	TDTPOWER
lists	TDT/S-TDT
lists	HAPLOBLOCKFINDER
lists	HAPMIXMAP
lists	Genotype-IBD Sharing Test
lists	LDGROUP
lists	LDHAT
lists	LDMAP
lists	LDHEATMAP
lists	LDSELECT
lists	LINKAGE
lists	LDSUPPORT
lists	FASTLINK
lists	LINKAGE - CEPH
lists	LSP
lists	Whap
lists	TREESCAN
lists	Graphical Overview of Linkage Disequilibrium
lists	MAIA
lists	MULTIMAP
lists	R/ADEGENET
lists	R/ENTROPY BLOCKER
lists	BEAM
lists	BMAPBUILDER
lists	POPGEN
lists	RTDT
lists	R/SPECTRAL-GEM
lists	R/STEPWISE
lists	HAPLOCLUSTERS
lists	TKMAP
lists	CLUMP
lists	FAMOZ
lists	INTEGRAYEDMAP
lists	SIBMED
lists	POOLSCORE
lists	LDA
lists	LAPSTRUCT
lists	BETA
lists	ALTree
lists	TRANSMIT
lists	ETDT
lists	R/TDTHAP
lists	RVTESTS
lists	S
lists	ET-TDT
lists	ILR
lists	MAPCREATOR
lists	MAPMAKER/SIBS
lists	MAP MANAGER QT
lists	MGA-MAPF2
lists	Pedigree-Draw
lists	FASTMAP (1)
lists	ASPEX
lists	PEDJAVA
lists	PEDPEEL
lists	SIMCOAL
lists	SNPHAP
lists	SNPHARVESTER
lists	SNP-HWE
lists	TAGSNP
lists	FASTMAP (2)
lists	FASTSLINK
lists	GASP
lists	GENOGRAM-MAKER
lists	GENEHUNTER++SAD
lists	GENEPI.JAR
lists	BDGEN
lists	TLINKAGE
lists	GENOME
lists	EASYPOP
lists	GENOMESIMLA
lists	TRAP
lists	CARTHAGENE
lists	ACT
lists	ADMIXMAP
lists	2DMAP
lists	ALBERT
lists	2SNP
lists	AGEINF
lists	ALLASS
lists	PEDIGREEQUERY
lists	PATH
lists	MULTIQTL
lists	SPERMSEG
lists	FASTER
lists	Platypus
lists	KIN
lists	SNP ASSISTANT
lists	GRONLOD
lists	COMBIN
lists	ARLEQUIN
lists	SEGPATH
lists	JENTI
lists	SCOUT
lists	HAPLOREC
lists	UNPHASED
lists	POWER
lists	HAPLO 1
lists	HAPLO 2
lists	CHIP2SPELL
lists	MAP MANAGER QTX
lists	G-MENDEL
lists	ASSOCIATIONVIEWER
lists	WHICHRUN
lists	GENECLASS
lists	MAREYMAP
lists	HELIXTREE
lists	SVCC
lists	GENEHUNTER-MODSCORE
lists	FAMHAP
lists	BAMA
lists	WEBQTL
lists	HAPLOVISUAL
lists	CASPAR
lists	GC/GCF
lists	MIXSCORE
lists	POWQ
lists	QTLNETWORK
lists	SIMULAPLOT
lists	SQTDT/SPDT
lists	FESTA
lists	BOTTLENECK
lists	PAP
lists	QUANTO
lists	R/QTL
lists	SNPEM
lists	GENEPOOL
lists	EPISTACY
lists	VITESSE
lists	LEA
lists	DMAP
lists	MOSCPHASER
lists	UMAKE
lists	TDT-AE
lists	HAPLOWSER
lists	STEPC
lists	RECORD
lists	QUTIE
lists	R/COMPOSITELD
lists	FINESSE
lists	R/EHP
lists	R/HCLUST
lists	STEPWISE
lists	genehunter-imprinting
lists	PBAT
lists	R/BARS
lists	HARDY
lists	R/ARP.GEE
lists	R/COVIBD
lists	STRAT
lists	TREELD
lists	TUNA
lists	SIBSIM
lists	IGG
lists	ALLELIX
lists	ALLEGRO
lists	ALOHOMORA
lists	ALP
lists	AMELIA
lists	ANALYZE
lists	ANCESTRY
lists	APE
lists	BARS
lists	APL-OSA
lists	APM
lists	ARIEL
lists	GENOMIZER
lists	ASP/ASPSHARE
lists	BIMBAM
lists	BIOIDE
lists	BIOLAD-DB
lists	BLADE
lists	BLOCK
lists	BOOLD
lists	BOOSTRAPPER
lists	BPPH
lists	BQTL
lists	DNABASER
lists	Calculator for Association with Two Stage design
lists	CC-QLS
lists	CCRAVAT
lists	CCREL
lists	CEPH2CRI
lists	CEPH2MAP
lists	EVOKER
lists	CFC
lists	CHECKHET
lists	MATLINK
lists	CHECKMATRIX
lists	CHIAMO
lists	CHROMOSCAN
lists	CHROMOSEG
lists	COPE
lists	HCLUST
lists	COVIBD
lists	CRIMAP-PVM
lists	CROSSFIND
lists	DGENE
lists	EHPLUS
lists	DHSMAP
lists	DISENTANGLER
lists	MAKEPED
lists	DOLINK
lists	DPPH
lists	GREGOR
lists	EAGLET
lists	EASYLINKAGE/EASYLINKAGE-PLUS
lists	EH
lists	EHAP
lists	EHP
lists	EMLD
lists	EPDT
lists	ERPA
lists	EXOMEPICKS
lists	R/META
lists	FASTEHPLUS
lists	FASTLINK
lists	FBAT
lists	FINETTI
lists	FIRSTORD
lists	FISHER
lists	GAIA
lists	GAP
lists	GAS
lists	GCHAP
lists	GDA
lists	GEMS
lists	GENECOUNTING
lists	GENEFINDER
lists	GENEHUNTER
lists	GENEHUNTER-IMPRINTING
lists	GENEHUNTER-PLUS
lists	GENEPOP
lists	GENERECON
lists	GENESPRING GT
lists	GENIE
lists	GENETIC POWER CALCULATOR
lists	GENETSIM
lists	GENOOM
lists	GENEVAR
lists	GENEWEAVER
lists	GENOCHECK
lists	GENOPROOF
lists	GENTOOLS
lists	GEST
lists	GEVALT
lists	GGT
lists	GHOST
lists	GLIDERS
lists	GLUE
lists	GMA
lists	GMCHECK
lists	GSMA
lists	GTOOL
lists	GWAPOWER
lists	HAP 2
lists	HAPAR
lists	HAPASSOC
lists	HAPBLOCK
lists	HAPGEN
lists	HAPINFERX
lists	HAPLOBLOCK
lists	HAPLOBUILD
lists	HAPLOPOOL
lists	HAPLORE
lists	HAPLO.STAT
lists	HAPLOT
lists	HAPLOTTER
lists	TWOLOC
lists	HAPLOTYPE ESTIMATION
lists	HAPLOTYPER
lists	HAPMINER
lists	HAP-SAMPLE
lists	HAPSIMU
lists	HIT
lists	HOMOG/HOMOGM
lists	HOTSPOTTER
lists	HPLUS
lists	HS-TDT
lists	HTR
lists	HTSNPER
lists	MDR-PDT
lists	INTERSNP
lists	IMPUTE
lists	NOPAR
lists	JLIN
lists	JOINMAP
lists	JPSGCS
lists	J/QTL
lists	KING
lists	LAMARC
lists	LINKAGE-IMPRINT
lists	LINKBASE
lists	LIPED
lists	LNKTOCRI
lists	LOCUSZOOM
lists	LOGINSERM ESTIHAPLO
lists	LOH-LINKAGE
lists	LOKI
lists	LOT
lists	L-POP
lists	LRP
lists	LRTAE
lists	LTSOFT
lists	MADMAPPER
lists	Marker And Gene Interpolation and Correlation
lists	MALDSOFT
lists	MAMA
lists	MANTEL-STRUCT
lists	MAP/MAP+/MAP+H/MAP2000
lists	MAPCHART
lists	MIDAS
lists	MAPDISTO
lists	MAPDRAW
lists	MAPINSPECT
lists	MAPL
lists	MARGARITA
lists	MDBLOCKS
lists	MAPMAKER/EXP
lists	MAPMAKER/HOMOZ
lists	MAPMAKER/QTL
lists	MAPQTL
lists	MCQTL
lists	MEGA2
lists	MEGASNPHUNTER
lists	MENDEL
lists	MERLIN
lists	MFLINK
lists	MINIMAC
lists	MINSAGE
lists	MITPENE
lists	MKGST
lists	MMDRAWER
lists	MLBGH
lists	MLD
lists	MLR-TAGGING
lists	PEDMANAGER
lists	SAGE
lists	MPDA
lists	MULTIDISEQ
lists	MULTIMAPPER
lists	MULTIMAPPER/OUTBRED
lists	MULTIPOPTAGSELECT
lists	MULTISIM
lists	MUTAGENESYS
lists	NOCOM
lists	NUCULAR
lists	ONEMAP
lists	OSIRIS
lists	P ACT
lists	PASS PEDIGREE
lists	PAWE
lists	PDA
lists	PDPSYS
lists	PDT
lists	PED
lists	PEDAGREE
lists	PEDCHECK
lists	PEDSTATS
lists	PEDSYS
lists	PEDVIZAPI
lists	PEER
lists	PHASE
lists	PLABSIM
lists	PL-EM
lists	POINTER
lists	POOL STR
lists	POWERMARKER
lists	POWERTRIM
lists	POWTEST
lists	PREPLINK
lists	PREST
lists	PROBMAX
lists	PROC QTL
lists	PROFILER
lists	PRT
lists	PSAT
lists	SAS/GENETICS
lists	PSEUDO
lists	PSEUDOMARKER
lists	PSEUDOMARKER.M
lists	R/LDHEATMAP
lists	QTL-ALL
lists	QTL Cartographer
lists	QTL EXPRESS
lists	QU-GENE
lists	RISCALW
lists	RC-TDT
lists	REAPER
lists	RELATIVE
lists	RELATIVEFINDER
lists	RELCHECK
lists	RELPAIR
lists	RELTYPE
lists	RHMAP
lists	ROMPREV
lists	ROSATTA SYLLEGO SYSTEM
lists	R/GAP
lists	R/HAPASSOC
lists	R/IBDREG
lists	R/LAPSTRUCT
lists	R/LDGROUP
lists	R/LUCA
lists	R/METASIM
lists	R/ONEMAP
lists	R/PIAGE
lists	R/POOLSCORE
lists	R/POPGEN
lists	R/QTLBIM
lists	R/SNP.PLOTTER
lists	SDMINP
lists	SELSIM
lists	SEQUENCE LD/SEQUENCE LDHOT
lists	SIBERROR
lists	SIBLINK
lists	SIB-PAIR
lists	SILCLOD
lists	SIMLA
lists	SNP CHART
lists	SIMLINK
lists	SIMPED
lists	SIMPLE
lists	SIMULA
lists	SIMULATE
lists	SIMUPOP
lists	SIMWALK
lists	START
lists	SKAT
lists	SLINK
lists	SMOOTH
lists	Suite of Nucleotide Analysis Programs
lists	SNAP 3
lists	SNPALYZE
lists	SNPFILE
lists	SNPLINK
lists	SNPP
lists	SNP.PLOTTER
lists	SNPTEST
lists	SPAM
lists	SPECTRAL-GEM
lists	SPERM
lists	SPIP
lists	SPLAT
lists	TAGSTER
lists	SPLINK
lists	SSAHASNP
lists	SUMSTAT
lists	SUP
lists	SWEEP
lists	TAGGER
lists	TFPGA
lists	TREESELECT
lists	UNKNOWN
lists	UTIL
lists	WHAIT
lists	ZAPLO
lists	HAPBLOCK 2
lists	PLABQTL
lists	TASSEL
lists	MCLEEPS
lists	SASGENE
lists	PANGAEA
lists	TOMCAT
lists	SCORE-SEQ
lists	SASQUANT
lists	QMSIM
lists	PIAGE
lists	PEDPACK
lists	INSEGT
lists	IBDREG
lists	GLFSINGLE/GLFTRIO/GLFMULTIPLES
lists	GGSD
lists	ECLIPSE
lists	CHROMSCAN
lists	COMPOSITELD
lists	BOOST
lists	ARP.GEE
lists	BOREL
lists	GASSOC
lists	MENDELSOFT
lists	PLINK/SEQ
lists	POLYPHEN
lists	SPREG
lists	MOLKIN
lists	PRESTO: Genetic Association Analysis Software
lists	ENDOG
lists	BEAGLECALL
lists	GWASELECT
lists	HEGESMA
lists	SNIPPEEP
lists	TAGIMPUTE
lists	SNPMSTAT
lists	SNP HITLINK
lists	MECPM
lists	R/FEST
lists	MAOS
lists	SUPERLINK
lists	PEDFIDDLER
lists	VG
lists	HAPSTAT
lists	QTDT
lists	GRIDQTL
lists	VH
lists	R/QTLDESIGN
lists	PYPOP
lists	ANTMAP
lists	MDR
lists	WEIGHTED FDR
lists	THESIAS
lists	DMLE
lists	SGS
lists	BAYESFST
lists	HWMET
lists	GRR
lists	AUTOSCAN
lists	TRIMHAP
lists	ILLUMINUS
lists	PELICAN
lists	HAPLOPAINTER
lists	HOMOZYGOSITYMAPPER
lists	GERMLINE
lists	PLINK
lists	MACH 1.0
lists	BEAGLE
lists	BIRDSUITE
lists	BREAKDANCER
lists	CAROL
lists	CASAVA
lists	CYRILLIC
lists	DINDEL
lists	GenABEL
lists	GATK
lists	PEDIGRAPH
lists	MADELINE
lists	METAL
lists	OLORIN
lists	PEDHUNTER
lists	POLYMUTT
lists	SAMTOOLS
lists	SNAP - SNP Annotation and Proxy Search
lists	STRUCTURE
lists	SVA
lists	SYZYGY
lists	VAAST
lists	Hapmix
lists	Ancestrymap
lists	Hmmer
lists	PROGENY
lists	VARSCAN
lists	MORGAN
lists	CMAP
lists	SIMHAP
lists	SIFT
lists	ANNOVAR
lists	Body Mass Index Calculator
lists	PolyPhen: Polymorphism Phenotyping
has parent organization	Feinstein Institute for Medical Research
has parent organization	Iowa State University; Iowa; USA

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