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


RESULTS
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
FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.
Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America. MorganNPrice@yahoo.com
Morgan N
MN
Price
Paramvir S
PS
Dehal
Adam P
AP
Arkin
D000465:Algorithms; D000818:Animals; D003201:Computers; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D005821:Genetic Techniques; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
D012336:RNA, Ribosomal, 16S