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WHAT'S NEW in
linkage analysis software list
(2005)

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• 12/23/05
  GENEHUNTER-MODSCORE
  HAPLOTYPE ESTIMATION

• 12/14/05
  A searchable list is being tested: http://www.animalgenome.org/soft/. Currently, this database contains all entries frozen at mid-October-2005.

• 11/07/05
  SIMPED : simulating haplotype and genotype data given a pedigree structure
  ENDOG :

• 10/21/05
  SIMHAP: simulation-based haplotypic analysis

• 10/14/05
  MADMAPPER : Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups.
  ALLEGRO version 2 is out in public domain: http://www.decode.com/software/allegro

• 10/12/05
  HAPLOT : a graphic program for presenting haplotype blocks
  HAPLO (2) : EM estimation of haplotype frequencies.

• 10/06/05
  SEGPATH : segregation analysis and path analysis

• 09/07/05
  HEGESMA : heterogeneity and genome search meta analysis

• 09/07/05
  ILR : imprinting linkage ratio

• 09/06/05
  LOT : linkage analysis of ordinal traits
  PAWE-3D : visualizing power for association with error

• 08/18/05
  LEA : likelihood-based estimation of admixture

• 08/11/05
  LAMARC : likelihood analysis with Metropolis algorithm using random coalescence
  FSTAT: calculate F-statistic and test gene diversities
  MULTISIM: analyze the numbers of individuals that founded new populations following a bottleneck or founding event

• 08/10/05
  more population genetics programs have been added

• 08/10/05
  LDSUPPORT :
  LOGINSERM_ESTIHAPLO:
  WHAP : SNP haplotype analysis
  HS-TDT: haplotype sharing TDT
  HAPLOREC : population-based haplotyping
  GENECLASS : select or exclude populations as origins of individuals
  WHICHRUN : using multilocus genotype to assign an individual to their most likely source population.
  GENEPOP : a population genetics software package
  BOTTLENECK : detect recent effective population size reductions from allele data frequencies
  PROBMAX: assigning unknown parentage in pedigree analysis
  SASGENE : a SAS program for segregation and linkage analysis in inbreeding populations
  SASQUANT : a SAS program for quantitative genetic analysis in inbreeding populations
  PARENTE : parentage inference
  SGS : spatial genetic software
  EASYPOP : simulate population genetics datasets
  GMA : genetic mixture analysis
  SPAM : genetic mixture analysis
  SIMCOAL : simulate coalescence
  POPDIST : population genetic distance
  PLABSIM : plant breeding simulations
  TFPGA : tools for population genetic analyses
  MANTEL-STRUCT : tests for population structure by Mantel tests
  EPISTACY : SAS code for identifying epistatically interacting QTLs

• 08/09/05
  the ftp field is combined with web, as less and less programs are distributed by ftp.
  DMAP (1), URP have been moved to obsolete programs list

• 08/09/05
  MULTIDISEQ : multipoint linkage analysis software which allows Marker-Marker LD
  PEDIGREEQUERY : pedigree drawing (document in Russian)
  MAIA : complex segregation analysis in animal pedigrees
  MGA-MAPF2: map QTLs in F-2 intercross in model organisms (document in Russian)
  MITPENE : analysis of mitochondrial diseases (document in Russian)
  AGEINF : infer the age of a rare, selectively-neutral mutation
  DMAP: disequilibrium mapping of a rare allele here
  HAPASSOC: haplotype inference using R
  LDHEATMAP : plots measures of pairwise linkage disequilibria for SNPs using R
  BARS : Bayesian Adaptive Regression Splines
  GC/GCF: genomic control
  HCLUST.R : clustering method to identify tagging SNPs using genotype data.
  ENTROPY BLOCKER : identify haplotype blocks
  MAPCREATOR : create gene maps
  COVIBD : refines linkage analysis of affected sibpairs by considering "covariates".
  BPPH : Berkeley method for Perfect Phylogeny Haplotyping
  DPPH : Direct method for Perfect Phylogeny Haplotyping
  2LD : two-locus LD
  FASTEHPLUS: faster EH+
  GENECOUNTING : gene-counting for haplotype analysis
  HAP (2) :
  GCHAP : gene-counting for haplotype analysis
  GS-EM: geno-spectrum EM method for haplotype phasing
  HAPSCOPE : analyzing functionally annotated haplotypes
  HPLUS

• 08/08/05
  CLUSTAG
  INTEGRATEDMAP
  TREESCAN

• 08/07/05
  TREELD
  GMCHECK

• 06/27/05
  SNP CHART

• 06/22/05
  ALOHOMORA : linkage analysis using 10k SNP array data
  SNP-HWE :
  PEDSTATS :

• 06/18/05
  GENETIC POWER CALCULATOR
  POWTEST
  POWER
  SNPEM : EM algorithm estimation of SNP haplotypes
  MAMA : multivariate association mapping algorithm
  HAPAR : haplotype inference by parsimony
  HAPINFERX :

• 06/09/05
  R/METASIM : R package for simulate a population of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization).

• 04/29/05
  SNPLINK : Multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal.

• 04/05/05
  VARIA : analyzing genetic variation on a genomic scale
  DCHIP LINKAGE : linkage analysis with SNP data

• 03/01/05
  MALDSOFT : admixture mapping

• 02/24/05
  MILD and BOOLD : calculation of LD

• 01/27/05
  EASYLINKAGE :
  LINKAGE-IMPRINT : LINKAGE allowing for imprinting

• 01/25/05
  MCQTL : multi-cross QTL mapping
  SIMUPOP : population simulation program

• 01/18/05
  HTSNPER : Haplotype Tagging SNPer

• 01/15/05
  POWERMARKER :

• 01/12/05
  SNPP : SNP processor

• 01/10/05
  LRTAE : likelihood ratio test allowing for errors

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