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jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors
Article first published online: 2 MAR 2012
DOI: 10.1111/j.2041-210X.2012.00194.x
© 2012 The Authors. Methods in Ecology and Evolution © 2012 British Ecological Society
Additional Information
How to Cite
Liu, X. (2012), jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors. Methods in Ecology and Evolution, 3: 624–627. doi: 10.1111/j.2041-210X.2012.00194.x
Publication History
- Issue published online: 30 JUL 2012
- Article first published online: 2 MAR 2012
- Received 9 December 2011; accepted 24 January 2012 Handling Editor: Oliver Pybus
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Keywords:
- neutrality test;
- next-generation sequencing;
- population genetics;
- population growth rate;
- population mutation rate;
- sequencing error
Summary
1. Next-generation sequencing (NGS) is being increasingly used in ecological and evolutionary studies. Though promising, NGS is known to be error-prone. Sequencing error can cause significant bias for population genetic analysis of a sequence sample.
2. We present jPopGen Suite, an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences. It is specially designed for data with a non-negligible error rate, although it serves well for ‘error-free’ data. It implements several methods for estimating the population mutation rate, population growth rate and conducting neutrality tests.
3. jPopGen Suite facilitates the population genetic analysis of NGS data in various applications and is freely available for non-commercial users at http://sites.google.com/site/jpopgen/.