fastStructure 1.0 – Inferring Population Structure from SNP Genotype data

fastStructure 1.0

:: DESCRIPTION

fastStructure is an algorithm for inferring population structure from large SNP genotype data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python
  • Numpy
  • Scipy
  • Cython
  • GNU Scientific Library

:: DOWNLOAD

 fastStructure

:: MORE INFORMATION

Citation

fastSTRUCTURE: variational inference of population structure in large SNP data sets.
Raj A, Stephens M, Pritchard JK.
Genetics. 2014 Jun;197(2):573-89. doi: 10.1534/genetics.114.164350

T-BAPS 1.0 – T-RFLP Bayesian Analysis of Population Structures

T-BAPS 1.0

:: DESCRIPTION

T-BAPS (T-RFLP Bayesian Analysis of Population Structures) is a free Windows package for performing clustering analysis using T-RFLP data. T-RFLP is a newly developed molecular fingerprinting technique mainly used to investigate population structures in microbial communities. Details of the method can be found in: Tang, J., Tao J., Urakawa, H. and Corander, J. T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 T-BAPS

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2007;6:Article30. Epub 2007 Nov 6.
T-BAPS: a Bayesian statistical tool for comparison of microbial communities using terminal-restriction fragment length polymorphism (T-RFLP) data.
Tang J, Tao J, Urakawa H, Corander J.

Clumpak 20150326 – Model-based Population Structure Analysis

Clumpak 20150326

:: DESCRIPTION

Clumpak (Cluster Markov Packager Across K) is a method that automates the postprocessing of results of model-based population structure analyses.

::DEVELOPER

Mayrose Lab, Tel Aviv University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX
  • Perl

:: DOWNLOAD

 Clumpak

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Feb 12. doi: 10.1111/1755-0998.12387.
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
Kopelman NM1, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I.

sNMF 1.2 – Inference of Population Structure using Sparse Non-negative Matrix Factorization algorithms

sNMF 1.2

:: DESCRIPTION

sNMF (Sparse Non-negative Matrix Factorization) is a fast and efficient method for the inference of Admixture Coefficients.

::DEVELOPER

Eric Frichot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 sNMF

:: MORE INFORMATION

Citation

Genetics. 2014 Apr;196(4):973-83. doi: 10.1534/genetics.113.160572. Epub 2014 Feb 4.
Fast and efficient estimation of individual ancestry coefficients.
Frichot E1, Mathieu F, Trouillon T, Bouchard G, François O.

LMM-Lasso – Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

LMM-Lasso

:: DESCRIPTION

LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 LMM-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):206-14. doi: 10.1093/bioinformatics/bts669.
A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.

fineSTRUCTURE 2.0.4 – Identify Population Structure using Dense Sequencing Data

fineSTRUCTURE 2.0.4

:: DESCRIPTION

fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.  By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals.

::DEVELOPER

Daniel Lawson

:: SCREENSHOTS

fineSTRUCTURE

:: REQUIREMENTS

  • Linux / Windows with  MinGW/ MacOsX

:: DOWNLOAD

  fineSTRUCTURE

:: MORE INFORMATION

Citation

Lawson, Hellenthal, Myers, and Falush (2012),
Inference of population structure using dense haplotype data“,
PLoS Genetics, 8 (e1002453).

SHIPS 1.1 – Spectral Hierarchical clustering for the Inference of Population Structure

SHIPS 1.1

:: DESCRIPTION

SHIPS is a non-parametric clustering algorithm that clusters individuals from a population into genetically homogeneous sub-populations from genotype data.

::DEVELOPER

Matthieu Bouaziz <matthieu.x.bouaziz@gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package

:: DOWNLOAD

  SHIPS

:: MORE INFORMATION

Citation

PLoS One. 2012;7(10):e45685. doi: 10.1371/journal.pone.0045685. Epub 2012 Oct 12.
SHIPS: Spectral Hierarchical clustering for the Inference of Population Structure in genetic studies.
Bouaziz M, Paccard C, Guedj M, Ambroise C.

AdmixKJump v2 – Identifying Population Structure in recently Diverged Groups

AdmixKJump v2

:: DESCRIPTION

AdmixKJump detects the number of populations in a cohort of samples with smaller sample sizes and shorter divergence times.

::DEVELOPER

O’Connor Evolutionary Genomics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 AdmixKJump

:: MORE INFORMATION

Citation

AdmixKJump: identifying population structure in recently diverged groups.
O’Connor TD.
Source Code Biol Med. 2015 Feb 3;10(1):2. doi: 10.1186/s13029-014-0031-1.

StructHDP – Inference of number of Clusters and Population Structure from Admixed Genotype data.

StructHDP

:: DESCRIPTION

StructHDP is a program for automatically inferring the population structure and number of clusters from a sample of admixed genotype data. It extends the model used by Structure to allow for a potentially infinite number of populations and then chooses the number of populations that best explain the data.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 StructHDP

:: MORE INFORMATION

Citation

StructHDP: automatic inference of number of clusters and population structure from admixed genotype data Suyash Shringarpure;
Daegun Won; Eric P. Xing
Bioinformatics 2011 27: i324-i332

Spectrum – Joint Bayesian Inference of Population Structure and Recombination Events

Spectrum

:: DESCRIPTION

Spectrum is a program for jointly inferring population structure and recombination events using multi-locus SNP haplotypes. Assuming a number of founder chromosomes, it infers the association of each individual with founders and generates an ancestral spectrum, which displays genetic population structure and reveals details of the genetic diversity of each individual with respect to recovered founder chromosomes. It also estimates empirical recombination rates and hotspots jointly with the population structure.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 Spectrum

:: MORE INFORMATION

Citation

Kyung-Ah Sohn and Eric P. Xing,
Spectrum:Joint Bayesian Inference of Population Structure and Recombination Events.
Bioinformatics. 2007 Jul 1;23(13):i479-89.