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  mlRho – a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes

Haubold, B., Pfaffelhuber, P., & Lynch, M. (2010). mlRho – a program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes. Molecular Ecology, 19(1), 277-284. doi:10.1111/j.1365-294X.2009.04482.x.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-D4D1-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000F-D4D2-8
Genre: Journal Article

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Haubold_2010.pdf (Publisher version), 240KB
 
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 Creators:
Haubold, Bernhard1, Author              
Pfaffelhuber, Peter, Author
Lynch, Michael, Author
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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Free keywords: bioinformatics/phyloinformatics; evolutionary theory; genomics/proteomics; population genetics – theoretical
 Abstract: Improvements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4Neμ), the sequencing error rate, and the population recombination rate (4Nec). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho.

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Language(s): eng - English
 Dates: 2010-02-10
 Publication Status: Published in print
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 Identifiers: eDoc: 452777
DOI: 10.1111/j.1365-294X.2009.04482.x
Other: 2753/S 39083
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Title: Molecular Ecology
Source Genre: Journal
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Pages: - Volume / Issue: 19 (1) Sequence Number: - Start / End Page: 277 - 284 Identifier: ISSN: 0962-1083 (print)
ISSN: 1365-294X (online)