{"name":"FastTree","description":"Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.","homepage":"https://www.microbesonline.org/fasttree/","biotoolsID":"fasttree","biotoolsCURIE":"biotools:fasttree","version":[],"otherID":[],"relation":[],"function":[{"operation":[{"uri":"http://edamontology.org/operation_0540","term":"Phylogenetic tree generation (from molecular sequences)"},{"uri":"http://edamontology.org/operation_0547","term":"Phylogenetic tree generation (maximum likelihood and Bayesian methods)"}],"input":[],"output":[],"note":null,"cmd":null}],"toolType":["Command-line tool"],"topic":[{"uri":"http://edamontology.org/topic_3293","term":"Phylogenetics"},{"uri":"http://edamontology.org/topic_0080","term":"Sequence analysis"}],"operatingSystem":["Linux","Windows"],"language":["C"],"license":null,"collectionID":["EBI Training Tools"],"maturity":null,"cost":null,"accessibility":null,"elixirPlatform":[],"elixirNode":[],"elixirCommunity":[],"link":[],"download":[],"documentation":[{"url":"https://www.microbesonline.org/fasttree/#How","type":["General"],"note":null}],"publication":[{"doi":"10.1093/molbev/msp077","pmid":"19377059","pmcid":"PMC2693737","type":[],"version":null,"note":null,"metadata":{"title":"Fasttree: Computing large minimum evolution trees with profiles instead of a distance matrix","abstract":"Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N 2) space and O(N 2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree. 2009 The Authors2009This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2009 The Authors.","date":"2009-07-01T00:00:00Z","citationCount":3611,"authors":[{"name":"Price M.N."},{"name":"Dehal P.S."},{"name":"Arkin A.P."}],"journal":"Molecular Biology and Evolution"}},{"doi":"10.1371/journal.pone.0009490","pmid":"20224823","pmcid":"PMC2835736","type":[],"version":null,"note":null,"metadata":{"title":"FastTree 2 - Approximately maximum-likelihood trees for large alignments","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. © 2010 Price et al.","date":"2010-03-10T00:00:00Z","citationCount":9314,"authors":[{"name":"Price M.N."},{"name":"Dehal P.S."},{"name":"Arkin A.P."}],"journal":"PLoS ONE"}}],"credit":[{"name":null,"email":"fasttree@microbesonline.org","url":null,"orcidid":null,"gridid":null,"rorid":null,"fundrefid":null,"typeEntity":"Person","typeRole":["Primary contact"],"note":null}],"owner":"ebi_training_import","additionDate":"2017-01-17T15:07:50Z","lastUpdate":"2024-11-24T14:34:57.624784Z","editPermission":{"type":"group","authors":["ardeleanadriandvm","ELIXIR-CZ"]},"validated":1,"homepage_status":0,"elixir_badge":0,"confidence_flag":null}