Migraine 0.5.4 – Maximum Likelihood Analysis of Population Genetic data

Migraine 0.5.4

:: DESCRIPTION

Migraine implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently  handled are allelic counts but sequences will be handled in the forthcoming version.

::DEVELOPER

Migraine team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 Migraine

:: MORE INFORMATION

Citation

Maximum-likelihood inference of population size contractions from microsatellite data.
Leblois R, Pudlo P, Néron J, Bertaux F, Reddy Beeravolu C, Vitalis R, Rousset F.
Mol Biol Evol. 2014 Oct;31(10):2805-23. doi: 10.1093/molbev/msu212

PopGenome 2.7.1 – Data Analysis in Population Genetics

PopGenome 2.7.1

:: DESCRIPTION

The PopGenome library provides data analysis in population genetics and is programmed in the powerful, open-source, statistical computing environment R. Several polymorphism statistics, such as the number of segregating sites and nucleotide or haplotype diversity based FST measurements can be calculated. In addition, PopGenome contributes a lot of neutrality statistics such as the Tajima D and Rozas R2 test. Testing of the significance of these statistics requires generating bootstrap samples from a neutral model using a coalescent approach.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PopGenome

:: MORE INFORMATION

Citation:

Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16.
PopGenome: an efficient Swiss army knife for population genomic analyses in R.
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ

DIVERGENOME – Bioinformatics Platform to Assist Population Genetics and Genetic Epidemiology Studie

DIVERGENOME

:: DESCRIPTION

DIVERGENOME is a bioinformatics platform to assist population genetics and genetic epidemiology studies performed by small- to medium-sized research groups.

DIVERGENOMEtools is a dynamic pipeline composed of a set of scripts, developed using a graph-based coordination algorithm and implemented in the programming language Perl.

::DEVELOPER

The Laboratory of Human Genetic Diversity (LDGH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 May;36(4):360-7. doi: 10.1002/gepi.21629. Epub 2012 Apr 16.
DIVERGENOME: a bioinformatics platform to assist population genetics and genetic epidemiology studies.
Magalhães WC1, Rodrigues MR, Silva D, Soares-Souza G, Iannini ML, Cerqueira GC, Faria-Campos AC, Tarazona-Santos E.

Tandem2 – Automated Microsatellite Allele Binning for Population Genetics Workflows

Tandem2

:: DESCRIPTION

All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. Tandem2 fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units.

::DEVELOPER

Michael Matschiner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Tandem2

:: MORE INFORMATION

Citation

Matschiner M, Salzburger W (2009)
TANDEM: integrating automated allele binning into genetics and genomics workflows.
Bioinformatics, 25(15), 1982-1983.

gPGA 1.0 – GPU Accelerated Population Genetics Analyses

gPGA 1.0

:: DESCRIPTION

gPGA (GPU Accelerated Population Genetics Analyses) is the extension of IM program that can effectively implement on Graphics Processing Unit (GPU).

::DEVELOPER

Chunbao Zhou (zhoucb@sccas.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 gPGA

:: MORE INFORMATION

Citation

gPGA: GPU Accelerated Population Genetics Analyses.
Zhou C, Lang X, Wang Y, Zhu C.
PLoS One. 2015 Aug 6;10(8):e0135028. doi: 10.1371/journal.pone.0135028. eCollection 2015.

CDPOP 1.2.21 – Spatially-explicit Cost Distance Population Genetics program

CDPOP 1.2.21

:: DESCRIPTION

CDPOP (Cost Distance POPulations) is a spatially-explicit simulator of gene-flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics.

::DEVELOPER

the Computational Ecology Lab, The University of Montana

:: SCREENSHOTS

CDPOP

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 CDPOP

:: MORE INFORMATION

Citation

Landguth EL, Cushman, SA (2010)
CDPOP: A spatially-explicit cost distance population genetics program.
Molecular Ecology Resources 10, 156-161

Geneland 4.0.5 – Statistical Analysis of Population Genetics data

Geneland 4.0.5

:: DESCRIPTION

Geneland is a computer program for statistical analysis of population genetics data. Its main goal is to detect population structure in form of systematic variation of allele frequency that can be detected from departure from Hardy-Weinberg and linkage equilibrium.

::DEVELOPER

Gilles Guillot

:: SCREENSHOTS

Geneland 

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package 

:: DOWNLOAD

 Geneland

:: MORE INFORMATION

Citation

G. Guillot, Mortier, F., Estoup, A.
Geneland: a computer package for landscape genetics
Molecular Ecology Notes, 5, 712-715, 2005.

SIMUPOP 1.1.4 – Population Genetics Simulation Environment

SIMUPOP 1.1.4

:: DESCRIPTION

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.

::DEVELOPER

Bo Peng, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX
  • Python

:: DOWNLOAD

 SIMUPOP

:: MORE INFORMATION

Citation

Bo Peng and Marek Kimmal (2005)
simuPOP: a forward-time population genetics simulation environment.
bioinformatics, 21(18): 3686-3687.

libsequence 1.8.4 – C++ Class Library for Population Genetics

libsequence 1.8.4

:: DESCRIPTION

libsequence is a C++ library designed to aid writing applications for genomics and evolutionary genetics. A large amount of the library is dedicated to the analysis of “single nucleotide polymorphism”, or SNP data.

::DEVELOPER

Thornton Lab at UC Irvine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 libsequence

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Nov 22;19(17):2325-7.
Libsequence: a C++ class library for evolutionary genetic analysis.
Kevin Thornton

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION