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