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PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490.

FastTree 2--approximately maximum-likelihood trees for large alignments.

Author information

  • 1Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America. MorganNPrice@yahoo.com

Abstract

BACKGROUND:

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.

METHODOLOGY/PRINCIPAL FINDINGS:

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.

CONCLUSIONS/SIGNIFICANCE:

FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.

PMID:
20224823
[PubMed - indexed for MEDLINE]
PMCID:
PMC2835736
Free PMC Article

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