harp 20140925 – Haplotype Analysis of Reads in Pools

harp 20140925

:: DESCRIPTION

harp : Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. harp implements an EM algorithm to calculate the frequencies of known haplotypes from pooled sequence data.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

harp

:: MORE INFORMATION

Citation

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
Darren Kessner; Tom Turner; John Novembre
Mol Biol Evol (2013) 30 (5): 1145-1158. doi: 10.1093/molbev/mst016

poolne_estim 1.0 – Estimating in Pool-Seq experiment the effective Diploid Size of Pools/replicates from SNP allele count data

poolne_estim 1.0

:: DESCRIPTION

poolne_estim is a program implementing a Markov Chain Monte Carlo algorithm to sample the posterior distribution of the different parameters underlying the Bayesian hierarchical model. It is primarily aimed at estimating in Pool-Seq experiment the effective diploid size of pools/replicates (e.g. identified by molecular barcodes) from SNP allele count data. Note that each pool (or replicate) are assumed to originate from the same population.

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

poolne_estim

:: MORE INFORMATION

Citation

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.
Gautier M, Foucaud J, Gharbi K, Cézard T, Galan M, Loiseau A, Thomson M, Pudlo P, Kerdelhué C, Estoup A.
Mol Ecol. 2013 Jul;22(14):3766-79. doi: 10.1111/mec.12360.

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