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FastTree 2--approximately maximum-likelihood trees for large alignments
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FastTree 2--approximately maximum-likelihood trees for large alignments
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Journal Article
FastTree 2--approximately maximum-likelihood trees for large alignments
2010
Overview
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.
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.
FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
/ Animals
/ Computational Biology/Macromolecular Sequence Analysis
/ Data Interpretation, Statistical
/ Evolutionary Biology/Bioinformatics
/ Humans
/ Methods
/ Molecular Biology/Molecular Evolution
/ Proteins
/ Pruning
/ RNA, Ribosomal, 16S - genetics
/ Sequence Alignment - methods
/ Software
/ Topology
/ Trees
