RvTests 1.9.9 – Rare Variant Test software for Next Generation Sequencing data

RvTests 1.9.9

:: DESCRIPTION

RvTests is a flexible software package for genetic association studies.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • C++ Compiler

:: DOWNLOAD

 RvTests

:: MORE INFORMATION

Citation

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data.
Zhan X, Hu Y, Li B, Abecasis GR, Liu DJ.
Bioinformatics. 2016 May 1;32(9):1423-6. doi: 10.1093/bioinformatics/btw079.

GWiS 1.1 – a Gene-based Test of Association

GWiS 1.1

:: DESCRIPTION

GWiS (a novel Gene-Wide Significance) test uses greedy Bayesian model selection to identify the independent effects within a gene, which are combined to generate a stronger statistical signal.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 GWiS

:: MORE INFORMATION

Citation

PLoS Genet. 2011 Jul;7(7):e1002177. doi: 10.1371/journal.pgen.1002177. Epub 2011 Jul 28.
Gene-based tests of association.
Huang H, Chanda P, Alonso A, Bader JS, Arking DE.

BaTS 1.0 – Measure and Test Phylogeny Trait Associations

BaTS 1.0

:: DESCRIPTION

BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

BaTS

:: MORE INFORMATION

Citation:

Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46

MOST 1.0 – Multivariate Outcome Score Test

MOST 1.0

:: DESCRIPTION

MOST (Multivariate Outcome Score Test) is able to analyze all the traits jointly. The framework is flexible in that it can handle both continuous and binary traits, or a mixture of them. In addition, it can accommodate family data, can adjust for covariates (such as ancestry variables, age, gender, etc.), and can be combined efficiently across studies with different designs. Furthermore, it has a built-in Monte Carlo procedure that can determine the genome-wide significance by taking into account the LD information among all the SNPs. Tur framework establishes a flexible platform for the analysis of multivariate-outcome association study, and provides a powerful tool for uncovering pleiotropic genetic variants.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

MOST

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Dec;37(8):759-67. doi: 10.1002/gepi.21759. Epub 2013 Nov 5.
A general framework for association tests with multivariate traits in large-scale genomics studies.
He Q1, Avery CL, Lin DY.

HIERFSTAT 0.04-10 – Package for R to Compute & Test Hierarchical F-statistics

HIERFSTAT 0.04-10

:: DESCRIPTION

HIERFSTAT is a package for R allowing to estimate F-statistics and variance components with the methods of moments for any number of levels in a hierarchy. The package also allows to test the significance of population differentiation using the likelihood ratio G-statistic or the variance components.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HIERFSTAT

:: MORE INFORMATION

Citation

Goudet, J. (2005)
Hierfstat, a package for R to compute and test hierarchical F-statistics.
Molecular Ecology Notes. 5: 184-186

ADMIXTOOLS 1.1 – Population Mixtures Test

ADMIXTOOLS 1.1

:: DESCRIPTION

ADMIXTOOLS is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ADMIXTOOLS

:: MORE INFORMATION

Citation

Genetics. 2012 Nov;192(3):1065-93. doi: 10.1534/genetics.112.145037. Epub 2012 Sep 7.
Ancient admixture in human history.
Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D.

Asymmetry 20060215 – Test Protein Sequence data for Substitutional Asymmetry

Asymmetry 20060215

:: DESCRIPTION

Asymmetry programs: AmbiguityRemover removes ambiguously aligned sites from protein sequence alignments, for input into AsymmetryCounter. AsymmetryCounter counts the number of amino acid subsitutions in each direction between pairs of protein sequences. AsymmetryScaler takes the results from AsymmetryCounter and summarizes substitutional asymmetry data in a single scale

::DEVELOPER

John H. McDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Asymmetry

:: MORE INFORMATION

Citation

McDonald, J.H., A.M. Grasso, and L.K. Rejto. 1999.
Patterns of temperature adaptation in proteins from Methanococcus and Bacillus.
Mol. Biol. Evol. 16: 1785-1790.

MultAssoc – Test of Association of a Disease with a Group of SNPs

MultAssoc

:: DESCRIPTION

MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 MultAssoc

:: MORE INFORMATION

Citation

Chatterjee N., Kalaylioglu Z., Moslehi R., Peters U., Wacholder S. (2006).
Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions.
American Journal of Human Genetics, Vol. 79, 1002-16.

AutocorQ – Characterise and Test the Spatial Autocorrelation of Quantitative Traits

AutocorQ

:: DESCRIPTION

AutocorQ is a simple software to characterise and test the spatial autocorrelation of quantitative traits. It computes Moran’s I statistics, can provide pairwise autocorrelation coefficient between individuals, and computes the slope of the linear regression of these coefficients on the spatial distance or its logarithm. The significance of the coefficients is assessed by random permutation tests.

::DEVELOPER

Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  AutocorQ

:: MORE INFORMATION

MANTEL-STRUCT 1.0 – Tests for Population Structure through the use of Mantel Tests

MANTEL-STRUCT 1.0

:: DESCRIPTION

MANTEL-STRUCT is a program that tests for population structure through the use of Mantel Tests.

::DEVELOPER

Mark P. Miller

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MANTEL-STRUCT

:: MORE INFORMATION

Citation:

Miller (1999),
MANTEL-STRUCT: a program for the detection of population structure via mantel tests“,
Journal of Heredity, 90:258-259.