new linkage software (2008-now)

An Alphabetic List
of
Genetic Analysis Software
WHAT'S NEW

(2008-now)

05/15/2009
PROC QTL : SAS procedure for mapping QTL
04/30/2009
GWAVA has been retired to the obsolete list.
03/05/2009
QMSIM : simulation of genetic architectures and population structures in livestock
12/27/2008
SUMSTAT
11/17/2008
GERMLINE
11/10/2008
LDA
11/03/2008
NUCULAR : splitting extended pedigrees to nuclear families
SIMM : a gene dropping program
GENEHUNTER++SAD : more robust to transmission ratio distortion in the context of allele sharing
09/15/2008
APL-OSA : association in the presence of linkage with ordered subset analysis
SIMULA :
SIMULAPLOT :
09/05/2008
SNAP(3) : Simulation of SNP haplotype data and phenotypic traits
SNP.PLOTTER : creates publishable-quality plots of LD p-values
MOCSPHASER: inferring haplotypes with both CNV alleles and SNP alleles
09/04/2008
PEDPEEL
08/06/2008
SNAP (2) : SNP Annotation and Proxy search
SWEEP : using long-range haplotype to detect natural selection
07/31/2008
HIT : haplotype inference technique
HAPLOVISUAL
PSAT : population stratification association test
GEVALT : genotype visualization and algorithmic tool
07/30/2008
BIMBAM : Bayesian IMputation-Based Association Mapping
EDCA : power calculator for extremely discordant and concordant sibpairs
GHOST : family-based genomewide association analysis with large pedigrees
IMPUTE : WTCCC's imputing genotype program, work with CHIAMO and HAPGEN
CHIAMO : genotype calling program for Affymetrix 500K chips
SNPTEST : work with CHIAMO, IMPUTE and GTOOL
GTOOL : work with SNPTEST and IMPUTE
MACH : Markov Chain haplotyper
P_ACT : R program for adjusting p-values in correlated tests
06/17/2008
QTL-ALL : QTL Analysis and Linkage Library
06/11/2008
RECORD : REcombination Counting and ORDering
SMOOTH :
06/04/2008
TUNA : testing untyped alleles
06/03/2008
GENIE : merged from PEDGENIE and HAPMC
05/21/2008
ANCESTRYMAP :
04/21/2008
MPDA : microarray pooled DNA analyzer
03/24/2008
PIAGE : power of indirect association studies of gene-environment interactions
03/05/2008
MUTAGENESYS :
QTLNETWORK : mapping and visualizing genetic network of QTs
JENTI : mining complex genealogies
02/19/2008
HAPLOBUILD :
02/11/2008
MULTIMAPPER :
MULTIMAPPER/OUTBRED :
J/QTL : Java GUI for R/QTL
PSEUDOMAKER.M : MATLAB code for QTL analysis of inbred line crosses.
QGENE : QTL mapping
MATLINK : MATLAB code for genetic linkage in exotic line-cross mating designs
PLABQTL : plant breeding QTL analysis