Tag: Genetics & Pedigree

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

FASTRUCT 1.01 – Analysis of Population Genetics and Individual Assignment

FASTRUCT 1.01

:: DESCRIPTION

FASTRUCT is a non-Bayesian implementation of the classical model with no-admixture uncorrelated allele frequencies. This new program relies on the Expectation-Maximization principle, and produces assignment rivaling other model-based clustering programs. In addition, it can be several-fold faster than Bayesian implementations. The software consists of a command-line engine, which is suitable for batch-analysis of data, and a MS Windows graphical interface, which is convenient for exploring data.

::DEVELOPER

the Computational and Mathematical Biology group in Grenoble

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 FASTRUCT

:: MORE INFORMATION

Citation

Chen C, Forbes F, François O (2006)
FASTRUCT: Model-based clustering made faster.
Molecular Ecology Notes Volume 6, Issue 4, pages 980–983,

ngsTools – Programs to Analyze NGS data for Population Genetics Purposes

ngsTools

:: DESCRIPTION

ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP or genotype calling, and are particularly suitable for low sequencing depth data.

::DEVELOPER

Matteo Fumagalli

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: 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.

parastructure 0.9 – Run the Population Genetics software STRUCTURE in Parallel on a Cluster

parastructure 0.9

:: DESCRIPTION

parastructure is a perl script collection to run the population genetics software STRUCTURE in parallel on a cluster (beowulf type).

::DEVELOPER

Jacques Lagnel (lagnel@her.hcmr.gr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 parastructure

:: MORE INFORMATION

SIMUPOP 1.1.10 – Population Genetics Simulation Environment

SIMUPOP 1.1.10

:: 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.

CDPOP 1.2.32 – Spatially-explicit Cost Distance Population Genetics program

CDPOP 1.2.32

:: 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

:: 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

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

EVOINFORMATICS GROUP

:: 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.

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.

Arlequin 3.5.2.2 – Population Genetics Data Analysis

Arlequin 3.5.2.2

:: DESCRIPTION

Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data).

The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Arlequin

:: MORE INFORMATION

Citation

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
Excoffier L, Lischer HE.
Mol Ecol Resour. 2010 May;10(3):564-7. doi: 10.1111/j.1755-0998.2010.02847.x.

libsequence 1.9.8 – C++ Class Library for Population Genetics

libsequence 1.9.8

:: 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

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