PSAT – Population Stratification Association Test

PSAT

:: DESCRIPTION

PSAT (Population Stratification Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease with stratification. Population stratification can be a serious obstacle in the analysis of genome-wide association studies. We have developed a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes account not only of the population structure but also of the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false positive rates than existing methods. In addition, it can be easily applied to whole genome association studies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows with Cygwin /Linux

:: DOWNLOAD

  PSAT

:: MORE INFORMATION

Citation

A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)

Baypass 2.2 – Genome-Wide Scan for Adaptive Differentiation and Association Analysis with Population-specific Covariables

Baypass 2.2

:: DESCRIPTION

The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Baypass

:: MORE INFORMATION

Citation

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.
Gautier M.
Genetics. 2015 Dec;201(4):1555-79. doi: 10.1534/genetics.115.181453.

SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

MimicrEE – Simulating Genotypes and Phenotypes in experimentally evolving populations

MimicrEE

:: DESCRIPTION

MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no ‘de novo’ mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

MimicrEE

:: MORE INFORMATION

SLiM 3.3.1 – Forward Population Genetic Simulation

SLiM 3.3.1

:: DESCRIPTION

SLiM (Selection on Linked Mutations) is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios.

::DEVELOPER

Messer Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX
:: DOWNLOAD

SLiM

:: MORE INFORMATION

Citation

SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model.
Haller BC, Messer PW.
Mol Biol Evol. 2019 Mar 1;36(3):632-637. doi: 10.1093/molbev/msy228.

PSIKO v2 – Infer Population Stratification on various levels in GWAS

PSIKO v2

:: DESCRIPTION

PSIKO (Population Structure Inference using Kernel-pca and Optimisation) is a software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++

:: DOWNLOAD

PSIKO

:: MORE INFORMATION

Citation

PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS.
Popescu AA, Huber KT.
Bioinformatics. 2015 Jul 2. pii: btv396.

SANTA-SIM 1.0 – Simulate the Evolution of Population of Gene Sequences Forwards through Time

SANTA-SIM 1.0

:: DESCRIPTION

SANTA-SIM is a forward-time simulator for gene sequences modeling a variety of mutation and selection processes.

::DEVELOPER

SANTA-SIM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

SANTA-SIM

:: MORE INFORMATION

Citation:

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Jariani A, Warth C, Deforche K, Libin P, Drummond AJ, Rambaut A, Matsen Iv FA, Theys K.
Virus Evol. 2019 Mar 8;5(1):vez003. doi: 10.1093/ve/vez003.

ngsTools 1.0.2 – Population Genetics Analyses from Next-generation Sequencing data

ngsTools 1.0.2

:: DESCRIPTION

ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty.

::DEVELOPER

ngsTools team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

ngsTools

:: MORE INFORMATION

Citation

ngsTools: methods for population genetics analyses from next-generation sequencing data.
Fumagalli M, Vieira FG, Linderoth T, Nielsen R.
Bioinformatics. 2014 May 15;30(10):1486-7. doi: 10.1093/bioinformatics/btu041.

pong – Fast Analysis and Visualization of Latent Clusters in Population Genetic data

pong

:: DESCRIPTION

pong is a freely available software package for post-processing output from clustering inference using population genetic data

::DEVELOPER

the Ramachandran Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • Python

:: DOWNLOAD

 pong

:: MORE INFORMATION

Citation

pong: fast analysis and visualization of latent clusters in population genetic data.
Behr AA, Liu KZ, Liu-Fang G, Nakka P, Ramachandran S.
Bioinformatics. 2016 Jun 9. pii: btw327.

ACG – Inference of Population History from Genetic data

ACG

:: DESCRIPTION

ACG (Ancestral Recombination Graph) is a graphical desktop application that allows genetics researchers to infer properties of a population based on genetic sequences sampled from it.

::DEVELOPER

Brendan O’Fallon (brendan.d.ofallon@aruplab.com).

:: SCREENSHOTS

ACG

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java

:: DOWNLOAD

 ACG

:: MORE INFORMATION

Citation:

ACG: rapid inference of population history from recombining nucleotide sequences.
O’Fallon BD.
BMC Bioinformatics. 2013 Feb 5;14:40. doi: 10.1186/1471-2105-14-40.