new genetic analysis software (2009-now)

An Alphabetic List
of
Genetic Analysis Software
WHAT'S NEW

(2009-now)

03/16/2012
ROMPREV : regression of offspring on midparent, revised
TRAP : Tiled Regression Analysis Package
01/04/2012
HOMOZYGOSITYMAPPER : web-based homozygosity mapping, for human, cattle, dogs, horses, mice, rats, sheep.
12/19/2011
SEQUENCE LD/SEQUENCE LDHOT :
12/01/2011
PASS PEDIGREE : a (commercial) pedigree drawing program
10/21/2011
ANNOVAR : functional annotation of genetic variants
10/20/2011
VAAST : Variant Annotation, Analysis and Search Tool
10/18/2011
HAPMIX : infer chromosome segments of distinct continental ancestry in admixed populations
MIXSCORE : combining genetic association and admixture association in admixed population
LTSOFT : a more powerful leverage of clinical-covariates in case-control association studies
TREESELECT : infer natural selection from differentiation between closely related populations
POLYPHEN : predicting damaging/deleterious mutations/polymorphisms
SIFT : sorting intolerant SNPs/mutations/polymorphisms from tolerant ones.
VARSCAN : variance calling from NGS data
BREAKDANCER : detect five types of structural variants (insertion, deletion, inversion, inter-chromosome translocation, intra-chromosome translocation) from NGS data
SAMTOOLS : this set of tools include SNP/indel calling programs
SYZYGY : SNP/indel calling from NGS data
CASAVA : commercial program (from Illunima) for SNP/indel calling for NGS data
SVA : sequence variant analyzer
DINDEL : indel detection from NGS data
PLAYPUS : SNP/indel calling from NGS data
SKAT : SNP-set kernel association test
10/17/2011
OLORIN : an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.
EVOKER : graphical tool for visualizing genotype intensity data
ARIEL : accumulation of rare variants integrated and extended locus-specific test
AMELIA : employs allele matching to analyse the effects of rare variants within a specific locus.
CAROL : a combined functional annotation score of non-synonymous coding variants
GLIDERS : HapMap based long-range LD search engine
GGSD : open-source, web-based and relational database driven data management software for large-scale genetic studies
CCRAVAT , QUTIE : Enabling the analysis of rare variants in large-scale case control and quantitative trait association studies.
GENEVAR : GENe Expression VARiation
ILLUMINUS : assigning SNP genotypes to Illumina data
MARGARITA : infers genealogies (by Ancestral Recombination Graph) from population genotype data to use these to map disease loci.
PEER : Bayesian factor analysis of high-dimensional phenotype data for eQTL
SSAHASNP : sequence search and alignment by hashing algorithm, to detect SNP/indel
BIRDSUITE : combined SNP/CNV analysis for Affymetrix genotyping data
GATK : genome analysis toolkit
PLINK/SEQ : complement to PLINK, but based in NGS data
SCORE-SEQ : score-type tests for associations with rare variants using sequencing data
SPREG : second phenotype regression analysis
TAGIMPUTE : impute of untyped SNPs
SNPMSTAT : genetic association with missing data
GWASELECT : variable selection in GWAS
MAOS : meta analysis with overlapping subjects
DISENTANGLER : visualization of LD and haplotypes
RVTEST : rare variants tests
UMAKE : variants calling pipeline from BAM files.
RELATIVEFINDER :
POLYMUTT : polymorphism and de novo mutation calls in families for sequencing data
MINIMAC : computationally efficient genotype imputation
LOCUSZOOM : viewing local association results
GLFSINGLE/GLFTRIO/GLFMULTIPLES : variant call for NGS data based on one/three/multiple GLF files.
EXOMEPICKS : suggests individuals for sequencing in a large pedigree
10/07/2010
KING : kinship-based inference for GWAS
10/04/2010
SNP HITLINK : pipeline for linkage analysis using SNPs
BOOST : Boolean operation-based screening and testing of interaction
MEGASNPHUNTER
09/28/2010
WHAIT: weighted haplotype test and an imputation-based test.
METAL: Meta Analysis Helper
GWAPOWER : genome-wide association power
R/META : R package for meta analysis
R/GENABEL : an R program GWAS analysis
BEAGLECALL : simultaneous genotype calling and haplotype phase inference
R/STEPWISE : identify recombination breakpoints
R/LUCA: Likelihood Under Covariate Assumptions
SOAP : short oligonucleotide analysis package for next generation sequencing
09/15/2010
JPSGCS: Java Programs for Statistical Genetics and Computational Statistics. newer update on GENEPI.JAR
09/1/2010
ANCESTRY : web-based user interface to compute individual ancestry
08/19/2010
MAREYMAP : estimating meiotic recombination
08/17/2010
G-MENDEL : a program from 1994
QTL CAFE : a program from 1998
GRIDQTL
R/QTLDESIGN
R/QTLBIM
MULTIQTL
06/15/2010
HAPSIMU :
04/26/2010
LAPSTRUCT : Laplacian eigenfunctions approach for population structure
SPECTRAL-GEM : spectral graph approach for genetic matching
04/07/2010
INTERSNP : genome-wide interaction analysis
02/19/2010
SNPHARVESTER: detecting epistatic interactions
02/11/2010
BEAM : Bayesian Epistasis Association Mapping
10/14/2009
SNIPPEEP : graphic interface to whole genome genotyping
ASSOCIATIONVIEWER: display SNP in a genetic context
10/09/2009
SNPFILE : a library and API for manipulating large SNP datasets
10/06/2009
CHIP2SPELL
HAPLOPOOL
IGG: integrate genotype for genetic studies
TAGSTER
09/30/2009
FEST
HAPLOWSER
PATH
09/08/2009
EAGLET : Efficient Analysis of Genetic Linkage -- Testing and Estimation
HAPMINER : mining the haplotypes by density-based clustering algorithm
MDR : multifactor dimensionality reduction
MDR-PDT : multifactor dimensionality reduction and pedigree disequilibrium test
GENOMESIMLA : generating data-sets with realistic LD patterns.
MECPM : Maximum Entropy Conditional Probability Modelling
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