popkin 1.3.0 – Estimate Kinship and FST under Arbitrary Population Structure

popkin 1.3.0

:: DESCRIPTION

The popkin (population kinship) R package estimates the kinship matrix of individuals and FST from their biallelic genotypes. Our estimation framework is the first to be practically unbiased under arbitrary population structures.

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

popkin

:: MORE INFORMATION

Citation

Ochoa, Alejandro, and John D. Storey. 2016b.
FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.
bioRxiv doi:10.1101/083923.

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