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Population genetic analysis software tools | Pool sequencing data analysis

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters.Source text:(Kofler et al., 2011) PoPoolation: a toolbox for population genetic analysis…
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KimTree
Desktop

KimTree

A method to estimate divergence times on a diffusion time scale from large…

A method to estimate divergence times on a diffusion time scale from large single-nucleotide polymorphism (SNP) data sets, conditionally on a population history that is represented as a tree.

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PoPoolation
Desktop

PoPoolation

Allows to compare allele frequencies for SNPs between two or more populations…

Allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. A toolbox specifically designed for the population genetic analysis of sequence…

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SNPGenie
Desktop

SNPGenie

Estimates evolutionary parameters from pooled next-generation sequencing…

Estimates evolutionary parameters from pooled next-generation sequencing single-nucleotide polymorphism data. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with…

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SelEstim
Desktop

SelEstim

A model-based method to distinguish putative selected polymorphisms from the…

A model-based method to distinguish putative selected polymorphisms from the background of neutral (or nearly neutral) ones and to estimate the intensity of selection at the former.

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npstat
Desktop

npstat

Implements some population genetics tests and estimators that can be applied to…

Implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.

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Pool-hmm
Desktop

Pool-hmm

A Python program for the estimation of allele frequencies and the detection of…

A Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool-Seq sample.

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Bayenv
Desktop

Bayenv

A Bayesian method that estimates the empirical pattern of covariance in allele…

A Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers, and then uses this as a null model for a test at individual SNPs.

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