{"doi":"10.1371/journal.pone.0009490","title":"FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments","abstract":"<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments. FastTree 2 is freely available at http://www.microbesonline.org/fasttree.","journal":"PLoS ONE","year":2010,"id":233,"datarank":24.08690507222999,"base_score":9.662434580678351,"endowment":9.662434580678351,"self_citation_contribution":1.4493651871017528,"citation_network_contribution":22.637539885128238,"self_endowment_contribution":1.4493651871017528,"citer_contribution":22.637539885128238,"corpus_percentile":98.4,"corpus_rank":491,"citation_count":15715,"citer_count":197,"citers_with_citation_signal":197,"citers_with_endowment":197,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2010-03-10","authors":[{"id":2171,"name":"Adam P. Arkin","orcid":"0000-0002-4999-2931","position":2,"is_corresponding":false},{"id":2172,"name":"Paramvir Dehal","orcid":"0000-0001-5810-2497","position":3,"is_corresponding":false},{"id":2169,"name":"Morgan N. Price","orcid":"0000-0002-4251-0362","position":0,"is_corresponding":true}],"reference_count":39,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}