mlRho version 2.9: Software for Estimating the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes

Bernhard Haubold, Peter Pfaffelhuber & Michael Lynch

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,$\delta$, and the population recombination rate, $\rho$ [1]. Please consult the documentation for further details.

Auxiliary Software

• ace2pro: Convert ACE files to profiles
• bow2pro: Convert bowtie files to profiles
• formatPro: Format profiles
• inspectPro: Inspect files generated by formatPro
• ms2dna: Convert output from Richard Hudson's coalescent simulation program ms to DNA sequence data
• sam2pro: Convert SAM files to profiles.
• sequencer: Simulate shotgun sequencing reads

Example Data

Ciona intestinalis profiles [2].

Old Version

• Version 1.7

Bibliography

1

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.

2

J.H. Kim, M.S. Waterman, and L.M. Li.
Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.
Genome Res, 17(7):1101-1110, Jul 2007.

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mlRho version 2.9: Software for Estimating the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes

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