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WHAT'S NEW in
linkage analysis software list
(2007)

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• 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

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