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.

FastPop – Infer Intercontinental Ancestry using Genetic data

FastPop

:: DESCRIPTION

FastPop is an efficient R package that fills the gap between Structure and Eigenstrat. It can: 1, generate PCA scores that identify ancestral origins and can be used for multiple studies; 2, infer ancestry information for data arising from two or more intercontinental origins.

::DEVELOPER

FastPop team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 FastPop

:: MORE INFORMATION

Citation

FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data.
Li Y, Byun J, Cai G, Xiao X, Han Y, Cornelis O, Dinulos JE, Dennis J, Easton D, Gorlov I, Seldin MF, Amos CI.
BMC Bioinformatics. 2016 Mar 9;17(1):122. doi: 10.1186/s12859-016-0965-1.

SPASIBA 0.0.2 – Spatial Continuous Assignment from Genetic Data

SPASIBA 0.0.2

:: DESCRIPTION

SPASIBA is an R package for spatial continuous assignment from genetic data.

::DEVELOPER

Gilles Guillot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 SPASIBA

:: MORE INFORMATION

Citation

Accurate continuous geographic assignment from low- to high-density SNP data.
Guillot G, Jónsson H, Hinge A, Manchih N, Orlando L.
Bioinformatics. 2015 Nov 28. pii: btv703.

Multilocus 1.3b – Analysis of Multi-locus Population Genetic Data

Multilocus 1.3b

:: DESCRIPTION

Multilocus has been written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, various linkage disequilibrium indices, and a measure of population differentiation, and allows one to search for subpopulations which do not share polymorphisms (and thus might be reproductively isolated). It includes a modification of the IA (Index of Association) metric that corrects the scaling effect seen when one applies the metric to different numbers of loci. In addition, there are randomization routines which allow one to test various null hypotheses.

::DEVELOPER

Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 Multilocus

:: MORE INFORMATION

PermutCpSSR 1.2.1 – Measures of Diversity and Differenciation from Haploid Population Genetic data

PermutCpSSR 1.2.1

:: DESCRIPTION

PERMUT computes measures of diversity and differenciation from haploid population genetic data, when a measure of the distance between haplotypes is available,and test whether the differentiation and diversity measures differ from the equivalent measures that do not take into account the distances between haplotypes

CpSSR computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered

::DEVELOPER

Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 PermutCpSSR

:: MORE INFORMATION

Citation

Mol Ecol. 1999 Oct;8(10):1593-602.
Rangewide variation of the maritime pine bast scale matsucoccus feytaudi duc. (Homoptera: matsucoccidae) in relation to the genetic structure of its host
Burban C, Petit RJ, Carcreff E, Jactel H.

QDB 2.6 – General Database Program suitable for Managing Genetic Data

QDB 2.6

:: DESCRIPTION

QDB (Quick DataBase) is a general database program suitable for managing genetic data which runs under Windows. QDB essentially consists of form-based facilities to edit data and facilities to generate reports using its own (idiosyncratic) language. There is provision to import and export data to and from text files and other DBF files. QDB basically works as a flat file database, but there is a facility for relational look- ups into other DBF files which can be used to obtain data in reports and in automatically calculated fields. Some aspects of QDB are modelled on Buttonware’s PC-File and in some areas there is near-compatibility between the programs.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

QDB

:: MORE INFORMATION

PBWT – Implementation of Positional Burrows-Wheeler Transform for Genetic data

PBWT

:: DESCRIPTION

The pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets.

::DEVELOPER

Richard Durbin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pbwt

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1266-72. doi: 10.1093/bioinformatics/btu014. Epub 2014 Jan 9.
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Durbin R.

adegenet 1.4-2 – Exploratory Analysis of Genetic data

adegenet 1.4-2

:: DESCRIPTION

adegenet is an  R package dedicated to the exploratory analysis of genetic data. It implements a set of tools ranging from multivariate methods to spatial genetics and genome-wise SNP data analysis.

::DEVELOPER

Thibaut Jombart

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  adegenet 

:: MORE INFORMATION

Citation

Jombart (2008),
adegenet: a R package for the multivariate analysis of genetic markers“,
Bioinformatics, 24:1403-1405.

bammds 20140602 – Create MDS plot of Populations for Genetic data

bammds 20140602

:: DESCRIPTION

bammds is a software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.

::DEVELOPER

bammds team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • R
  • Perl

:: DOWNLOAD

 bammds

:: MORE INFORMATION

Citation

bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS).
Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R.
Bioinformatics. 2014 Jun 28. pii: btu410.