Tag: Recombination Rate

mlRho 2.9 – Estimate the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes

mlRho 2.9

:: DESCRIPTION

mlRho takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, $\theta$, the sequencing error $\epsilon$, the zygosity correlation, and the population recombination rate, $\rho$

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • C Compiler

:: DOWNLOAD

 mlRho

:: MORE INFORMATION

Citation

B. Haubold, P. Pfaffelhuber, and M. Lynch.
mlRho: A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.
Molecular Ecology, 19:277-284, 2010.

LDhelmet 1.10 – Fine-scale Recombination Rate Estimation

LDhelmet 1.10

:: DESCRIPTION

LDhelmet is a software program for statistical inference of fine-scale crossover recombination rates from population genetic data.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 LDhelmet

:: MORE INFORMATION

Citation

Chan, A.H., Jenkins, P.A., and Song, Y.S.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
PLoS Genetics, vol. 8 no. 12 (2012) e1003090.

FastEPRR 2.0 – Fast Estimation of Population Recombination Rates

FastEPRR 2.0

:: DESCRIPTION

FastEPRR is an extremely fast open-source software package to estimate population recombination rate based on intraspecific DNA polymorphism data.

::DEVELOPER

Evolutionary Genomics Lab, PICB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

 FastEPRR

:: MORE INFORMATION

Citation

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era.
Gao F, Ming C, Hu W, Li H.
G3 (Bethesda). 2016 Mar 30. pii: g3.116.028233. doi: 10.1534/g3.116.028233

MareyMap 1.3.4 – Recombination Rate Estimator

MareyMap 1.3.4

:: DESCRIPTION

MareyMap is a meiotic recombination rate estimation program. It is based on R and features a graphical interfcace in tcl/tk. MareyMap comes with an extensive dataset and several interpolation methods. The user may also use MareyMap with his own data.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MareyMap

:: MORE INFORMATION

Citation

Rezvoy, C., Charif, D., Gueguen, L., Marais, G.A.B. (2007)
MareyMap: A R-based tool with graphical interface for estimating recombination rate.
Bioinformatics 23: 2188-2189.”

InferRho 1.0 – Recombination Rate Inference

InferRho 1.0

:: DESCRIPTION

InferRho is a MCMC based program for jointly estimating the crossing-over and gene-conversion parameters from population genomic datasets under a Bayesian framework.

::DEVELOPER

Rannala Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 InferRho

:: MORE INFORMATION

Citation

Wang, Y., and B. Rannala, 2009
Population genomic inference of recombination rates and hotspots
PNAS 106 no. 15 , 6215–6219

COB – Estimating Recombination Rates

COB

:: DESCRIPTION

COB is a parsimony-based method of computing likelihoods accurately under the coalescent with recombination.

::DEVELOPER

Rune Lyngsø

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 COB

:: MORE INFORMATION

Citation

Lyngsø, R., Song, Y.S., and Hein, J.
Accurate computation of likelihoods in the coalescent with recombination via parsimony.
Lect Notes Comput Sci. 2008; 4955(LNBI): 463–477.

PHASE 2.1.1 – Haplotype Reconstruction & Recombination Rate Estimation

PHASE 2.1.1

:: DESCRIPTION

PHASE is a software for haplotype reconstruction, and recombination rate estimation from population data.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

PHASE ; Manual

:: MORE INFORMATION

The software is free for non-commercial use, and may be licensed for commercial use.