new linkage software (2007-now)

An Alphabetic List
of
Genetic Analysis Software
WHAT'S NEW

(2007-now)

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
11/21/2007
PEDVIZAPI : Java API visualization of large pedigrees
ONEMAP
11/16/2007
LDGROUP
ADGENET
MAPDRAW
10/26/2007
BIOIDE : Biomedical Integrated Discovery Environment
ROSETTA SYLLEGO SYSTEM : genetic data management and analysis system
PRESTO :
09/14/2007
FAMHAP
HAPSTAT : haplotype-disease association
GAS2 : statistical significance in two-stage genomewide association studies
SQTL : semiparametric QTL mapping in general pedigree
SVCC : semiparametric variance-component method for censored data
SQTDT/SQPDT : semiparametric TDT/PDT
09/04/2007
GENEPOOL
07/12/2007
EPDT : extended pedigree linkage disequilibrium test
PDA : pooled DNA analyzer
MENDELSOFT : detecting Mendelian errors in marker data
06/29/2007
CC-QLS : case-control quasi-likelihood score test
STEPC : statistical explanation for positional cloning
05/09/2007
GENOMIZER : an integrated analysis system for genome-wide association data
PLINK : a whole-genome association analysis toolset
04/29/2007
UTIL: statistical genetics utility programs, replacing "linkage utilities"
04/27/2007
BAYESFST: Bayesian estimation of the coancestry coefficient F_ST
HWMET : Bayesian estimation of the inbreeding coefficient f
LAMBDAA :
LDMET : Bayesian estimation of gametic disequilibrium coefficients
HAP-SAMPLE: simulating SNP genotypes for case-control and affected-child trio studies
04/23/2007
LDHAT : analysis of recombination rates
01/26/2007
HAPMC : Monte Carlo procedure to correctly perform haplotype anlysis
GENEPI.JAR : a set of Java programs for genetic epidemiology analysis
01/25/2007
APE : allelic path explorer
GENOME : simulate genome sequence with Wright-Fisher's neutral model
GWAVA : genome-wide association visual analyzer
VARIA has been renamed GENESPRING GT
01/24/2007
CHROMOSEG : simulates and plots ancestral recombination graphs
MDBLOCKS : minimum description length method for haplotype blocks
SPIP : simulate pedigrees in populations
FPG : full parental genotyping in salmon
PGR is moved to the obsolete program list
01/23/2007
GEST : gene x environment interaction and stability
MAPCOMP is renamed MAPINSPECT
MAP MANAGER CLASSIC is replaced by MAP MANAGER QT .
01/22/2007
ANTMAP : ordering larger number of markers by "Ant Colony Optimization" method
01/10/2007
IBDREG : linkage with covariates by regression method
HWESTRATA : exact stratified test for HWE for diallelic markers
COMPOSITELD : composite measure of LD
ARP.GEE : estimate a trait-locus position and its genetic effects for affected relative pairs
FREENA : perform three population genetics tasks on microsatellites
HAPBLOCK (2) : STATA module for haplotype block analysis
01/05/2007
WEIGHTED_FDR.R : R script for calculating weighted false discovery rate
01/03/2007
POOLSCORE : R script for case-control analysis using DNA pool
HAPMIXMAP : modeling haplotypes similar to the FASTPHASE program
POOL_STR : pooling alleles of single tandem repeat markers
ALBERT : estimating risk in trios.
MOLKIN : genetic analysis of populations using molecular coancestry information