pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree |
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Authors: | Frederick A Matsen Robin B Kodner E Virginia Armbrust |
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Institution: | 1.Computational Biology Program,Fred Hutchinson Cancer Research Center,Seattle, Washington,USA;2.School of Oceanography, University of Washington,Seattle, Washington,USA;3.Friday Harbor Laboratories,University of Washington,Washington,USA |
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Abstract: | Background Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown
sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from
next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement,"
where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way
to bring the inferential power offered by likelihood-based approaches to large data sets. |
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