FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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Price, Morgan N. ; S. Dehal, Paramvir ; Arkin, Adam P.
  • Publisher: Figshare
  • Related identifiers: doi: 10.1371/journal.pone.0009490
  • Subject: Medicine | Molecular Biology | Evolutionary Biology | fasttree | maximum-likelihood | trees | alignments

<div><h3>Background</h3><p>We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability.</p><h3>Methodology/Principal Findings</h3><p>Where FastTree 1 used nearest-neighbor interchanges (NNIs) and the minimum-evolution criterion to improve the tree, FastTree 2 adds minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood NNIs. FastTree 2 uses heuristics to restrict the search for better trees and estimates a rate of evolution for each site (the “CAT” approximation). Nevertheless, for both simulated and genuine alignments, FastTree 2 is slightly more accurate than a standard implementation of maximum-likelihood NNIs (PhyML 3 with default settings). Although FastTree 2 is not quite as accurate as methods that use maximum-likelihood SPRs, most of the splits that disagree are poorly supported, and for large alignments, FastTree 2 is 100–1,000 times faster. FastTree 2 inferred a topology and likelihood-based local support values for 237,882 distinct 16S ribosomal RNAs on a desktop computer in 22 hours and 5.8 gigabytes of memory.</p><h3>Conclusions/Significance</h3><p>FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at <a href="http://www.microbesonline.org/fasttree">http://www.microbesonline.org/fasttree</a>.</p></div>
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