Tag: Population Genetic

GenAlEx 6.51b2 – Population Genetic Analysis within Microsoft Excel

GenAlEx 6.51b2

:: DESCRIPTION

GenAlEx (Genetic Analysis in Excel) is a user-friendly cross-platform package for population genetic analysis that runs within Microsoft Excel(TM). GenAlEx enables population genetic data analysis of codominant, haploid and binary genetic data providing analysis tools applicable to plants, animals and microorganisms. GenAlEx was originally developed as a tool to assist us in our teaching of population genetic analysis, and is now widely used by university teachers and researchers around the world. In GenAlEx 6, we are pleased to introduce many new features for both teachers and researchers.

::DEVELOPER

GenAlEx Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Microsoft Excel(TM)

:: DOWNLOAD

GenAlEx

:: MORE INFORMATION

Citation

Peakall, R., Smouse, P.E., 2006.
GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research.
Molecular Ecology Notes 6, 288-295.

SFS_CODE 0.9 – Forward Population Genetic Simulation program

SFS_CODE 0.9

:: DESCRIPTION

SFS_CODE  (Simulating Finite Sites under COmplex Demographic Events) can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects.

SFS_CODE Online version

::DEVELOPER

The Hernandez Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SFS_CODE

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 1;24(23):2786-7. doi: 10.1093/bioinformatics/btn522. Epub 2008 Oct 7.
A flexible forward simulator for populations subject to selection and demography.
Hernandez RD.

CLUMPP 1.1.2 – Label Switching and Multimodality problems in Population-genetic Cluster Analyses

CLUMPP 1.1.2

:: DESCRIPTION

CLUMPP (CLUster Matching and Permutation Program) is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible.

::DEVELOPER

Rosenberg lab at Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 CLUMPP

:: MORE INFORMATION

Citation

CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.
Jakobsson M, Rosenberg NA.
Bioinformatics. 2007 Jul 15;23(14):1801-6.

BayeScan 2.1 – Detect Natural Selection from Population-base Genetic Data

BayeScan 2.1

:: DESCRIPTION

BayeScan ( (BAYEsian genome SCAN for outliers) ) aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model. One of the scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient. Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BayeScan

:: MORE INFORMATION

Citation

Mol Ecol. 2011 Apr;20(7):1450-62. doi: 10.1111/j.1365-294X.2011.05015.x.
Enhanced AFLP genome scans detect local adaptation in high-altitude populations of a small rodent (Microtus arvalis).
Fischer MC, Foll M, Excoffier L, Heckel G.

PGDSpider 2.1.1.5 – Data conversion tool for Population Genetic and Genomics Programs

PGDSpider 2.1.1.5

:: DESCRIPTION

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • java

:: DOWNLOAD

 PGDSpider

:: MORE INFORMATION

Citation

Lischer HEL and Excoffier L (2012)
PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs.
Bioinformatics 28: 298-299.

ForwSim – Population Genetic Simulators

ForwSim

:: DESCRIPTION

FORWSIM is a forward-time simulation programs for the standard neutral model.

::DEVELOPER

Badri Padhukasahasram (pkbadri@yahoo.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Mac OsX
  • GCC

:: DOWNLOAD

 ForwSim

:: MORE INFORMATION

Citation

Exploring population genetic models with recombination using efficient forward-time simulations.
Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M.
Genetics. 2008 Apr;178(4):2417-27.

popgen 0.2 – Population Genetic Simulations & Numerical Analysis

popgen 0.2

:: DESCRIPTION

popgen conducts various numerical analyses and simulations in population genetics and evolutionary theory.

::DEVELOPER

REVELL LAB @ UMASS BOSTON

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Windows /Linux
  • R Package

:: DOWNLOAD

 popgen

:: MORE INFORMATION

MSMS 3.2rcb122 / MSMSPlay – Coalescent Simlation tool with Selection / Exploration of Basic Population Genetic Theory

MSMS 1.3 / MSMSPlay

:: DESCRIPTION

MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios.

MSMSPlay is a GUI designed for simple exploration of basic population genetic theory. Its meant for exploratory runs with some useful output in an interactive fashion.

::DEVELOPER

The Mathematics and BioSciences Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MSMS / MSMSPlay

:: MORE INFORMATION

Citation

Ewing G. and Hermisson J. (2010).
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065.

Selection 3.2 – Demonstrate Simple Population Genetic Effects of Selection

Selection 3.2

:: DESCRIPTION

Selection is a simulation program which demonstrates simple population genetic effects of selection, mutation, migration and drift in a single-locus, two-allele model. The program offers both an analytic and a stochastic model with full user control of the simulation parameters and a variety of options in the onscreen display. Students can control the relative fitnesses of the two alleles, mutation and migration rates, as well as population size. The display can be set to overlay multiple simulation runs, and the scale can be altered to view different parts of a given simulation run in greater detail.

::DEVELOPER

The Queller/Strassmann Research Group at Washington University in St. Louis

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac

:: DOWNLOAD

 Selection

:: MORE INFORMATION

Formatomatic 0.8.1 – Population Genetic File Creator and Converter

Formatomatic 0.8.1

:: DESCRIPTION

Formatomatic creates infiles for several population genetic analysis programs from csv, genepop or convert* (excel) files. It only handles diploid microsatellite data for now.

::DEVELOPER

Nick Manoukis

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 Formatomatic

:: MORE INFORMATION

Citation

Manoukis, N.C. 2007.
FORMATOMATIC: A program for converting diploid allelic data between common formats for population genetic analysis.
Molecular Ecology Notes, 7(4):592 – 593

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