HOTSPOTTER 1.2.1 – Identify Recombination Hotspots

HOTSPOTTER 1.2.1

:: DESCRIPTION

HOTSPOTTER is a software for identifying recombination hotspots from population SNP data.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

HOTSPOTTER

:: MORE INFORMATION

Citation

N Li and M Stephens. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics, 165(4)2213-2233, 2003.

 

SCAT 1.0.2 – Smoothed & Continuous AssignmenTs

SCAT 1.0.2

:: DESCRIPTION

SCAT (Smoothed and Continuous AssignmenTs) implements a Bayesian statistical method for estimating allele frequencies and assigning samples of unknown (or known) origin across a continuous range of locations, based on genotypes collected at distinct sampling locations. In brief, the idea is to assume that allele frequencies vary smoothly in the study region, so allele frequencies are estimated at any given location using observed genotypes at near-by sampling locations, with data at the nearest sampling locations being given greatest weight.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

SCAT

:: MORE INFORMATION

Citation

S K Wasser, A M Shedlock, K Comstock, E A Ostrander, B Mutayoba, and M Stephens. Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc Natl Acad Sci U S A, 41:14844-14852, 2004.

PHASE 2.1.1 – Haplotype Reconstruction & Recombination Rate Estimation

PHASE 2.1.1

:: DESCRIPTION

PHASE is a software for haplotype reconstruction, and recombination rate estimation from population data.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

PHASE ; Manual

:: MORE INFORMATION

The software is free for non-commercial use, and may be licensed for commercial use.

 

fastPHASE 1.4.0 – Haplotype Reconstruction & Estimating Missing Genotypes

fastPHASE 1.4.0

:: 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

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

fastPHASE

:: 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

SFA 1.0 – Sparse Factor Analysis

SFA 1.0

:: DESCRIPTION

SFA (Sparse Factor Analysis) uses ECME to compute a sparse, low-rank matrix factorization for a given matrix.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

SFA

:: 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.

HaploPowerCalc 1.0 – Haplotype Estimation

HaploPowerCalc 1.0

:: 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

  • Linux
  • PHASE

:: DOWNLOAD

HaploPowerCalc

:: MORE INFORMATION

N/A

multiPopTagSelect 1.1 – Select Tagging Single-nucleotide Polymorphisms

multiPopTagSelect 1.1

:: 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

  • Linux / Windows / Max OS X
  • Perl

:: DOWNLOAD

multiPopTagSelect

:: 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.

LCMT – Multiple Genetic Markers Association test

LCMT

:: 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

FBAT-Toolkit Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux/ Sunsparc stations

:: DOWNLOAD

LCMT

:: MORE INFORMATION

References

H zhou, L wei, X Xu, X Xu (2006) Combining association tests across multiple genetic markers in case-control studies

XWXW – Linkage Analysis of Quantitative Traits

XWXW

:: 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

FBAT-Toolkit Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux/ Sunsparc stations

:: DOWNLOAD

XWXW

:: 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