:: DESCRIPTION
PHASE is a software for haplotype reconstruction, and recombination rate estimation from population data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The software is free for non-commercial use, and may be licensed for commercial use.
:: DESCRIPTION
fastPHASE is a software for haplotype reconstruction, and estimating missing genotypes from population data. fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The software is free for non-commercial use, and may be licensed for commercial use.
Citation
Scheet, P and Stephens, M (2006) A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. Am J Hum Genet 78: 629-644
:: DESCRIPTION
SFA (Sparse Factor Analysis) uses ECME to compute a sparse, low-rank matrix factorization for a given matrix.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Engelhardt BE, Stephens M (2010)
“Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.”
PLoS Genetics 6(9):e1001117.
:: DESCRIPTION
HaploPowerCalc is a tool for estimating power to detect disease association by a set of markers (e.g. a tag SNP panel or SNPs on an array), at any user-specified polymorphic site(s), under arbitrary disease model and sample sizes. It is intended for users who wish to estimate the power (or sample sizes required to obtain adequate power) in their association study. HaploPowerCalc uses an approach based on haplotype-sampling.
::DEVELOPER
Dr. Deborah Nickerson’s lab at the University of Washington
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
N/A
:: DESCRIPTION
multiPopTagSelect attempts to select a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. Specifically, it processes the output of tagSNP selection algorithms that designate bins of nearly equivalent SNPs, such that choosing (and typing) one SNP from each bin is sufficient to capture all associations observed in the data. Most of this documentation concerns one particular tagSNP selection method known as ldSelect, but multiPopTagSelect can also be used with other methods whose output has been converted into ldSelect format. This program can optimize SNP selection across any number of populations, and it can be applied to genomic regions ranging from small genes to entire chromosomes.
::DEVELOPER
Dr. Deborah Nickerson’s lab at the University of Washington
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Howie BN, Carlson CS, Rieder MJ, Nickerson DA. Efficient selection of tagging single-nucleotide polymorphisms in multiple populations. Hum Genet. 2006 120(1):58-68.
:: DESCRIPTION
LCMT is a small program performing “combining” association test over multiple genetic markers.LCMT implements the “combining” method for the association test over multiple genetic markers. It optimally utilizes the information from those markers. It is preferred over several competing tests, such as the Bonferroni procedure, the permutation procedure, the traditional χ2 procedure, the regression procedure (Hotelling T2 test) and the haplotype-based test.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
References
H zhou, L wei, X Xu, X Xu (2006) Combining association tests across multiple genetic markers in case-control studies
:: DESCRIPTION
XWXW implements the Unified Haseman-Elston method for non-parametric linkage test with quantitative traits. It optimally utilizes the information from a sib-pair. It is uniformly more powerful than both the classical H-E method and the revistited H-E method. Program GENIBD from SAGE or GeneHunter2 is required for sib-pair ibd estimation.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
References
Xu X, Palmer LJ, Horvath S, and Wei LJ. Combining Multiple Phenotypic Traits Optimally for Detecting Linkage with Sib-pair Observations. (2001) Genet. Epidemiol.
Xu X., Weiss S. Xu X., Wei LJ. A unified Haseman-Elston regression method for testing linkage with quantitative trait (2000) Am. J. Hum. Genet. 67: 1025-8
:: DESCRIPTION
The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.
