Online tools Population Genetics

Online Tools

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ABCreg implements the linear regression approach to "Approximate Bayesian Computation" ...

Author(s)

Kevin Thornton


Version

1


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AFCR

Tool

 

This procedure is aimed to reduce the dimensionality of a genotypic data to visualize them in a subspace of 2 or 3 dimensions. Adapted from ca R-package by Nenadic and Greenacre.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


AFCRPOP

Tool

 

This procedure is aimed to reduce the dimensionality of a genotypic data to visualize them in a subspace of 2 or 3 dimensions. Adapted from ca R-package by Nenadic and Greenacre. Pseudo-individus are constructed for each population by summing individual alleles counts. These values are then added to the matrix of individual alleles and analysed with ca() while setting only the pseudo-individus as active elements.

Author(s)

Unknown


Version

1


Subsections

Tool


Co-dominant Markers pair-wise genetic distances.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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Co-dominant Markers permutation on pair-wise distances.

Author(s)

Khalid Belkhir


Version

1


Subsections

Tool


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First cfit online tool

Author(s)

Unknown


Version

1


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A little test for Auto_Pise .

Author(s)

Unknown


Version

1


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Genepop implements a mixture of traditional methods and some more focused developments: It computes exact tests for Hardy-Weinberg equilibrium, for population erentiation and for genotypic disequilibrium among pairs of loci; It computes estimates of F-statistics, null allele frequencies, allele size- based statistics for microsatellites, etc., and of number of immigrants by Barton and Slatkin s 1986 private allele method; It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including condence intervals for neighborhood size.

Author(s)

François Rousset


Version

4.0


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IM program for fitting the Isolation w/ Migration model using a MCMC method : IM is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

1


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IMa program for fitting the Isolation w/ Migration model using a MCMC method : IMa is a program, written by Jody Hey and Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations

Author(s)

Hey and Nielsen


Version

2.0


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LS TEST

Tool

 

This is a simple test of Pise

Author(s)

Julien V, Jimmy L


Version

1


Subsections

Tool


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Apps


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Used in order to perform a Mantel test based on two distance matrix. The number of permutations can be specified. An HTML file containing a graphical representation of the statistic Z distribution is generated.

Author(s)

Sara Jaillet & Khalid Belkhir


Version

1


Subsections

Tool


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This OnlineTool is a wrapper for structure software http://pritch.bsd.uchicago.edu/structure.html

It is the same wrapper as structure_param, however, you can specify a maximum and a minimum value for K (structure_param is an OnlineTool for structure but you have to give extraparam and mainparam file).

Author(s)

Pritchard, Stephens, Donnely, Falush, Hubisz


Version

2.3.4


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First cfit online tool

Author(s)

Unknown


Version

1


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The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

Author(s)

Pritchard, Stephens, Donnelly, Hubisz, Falush


Version

2.3.4


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