FastTree swMATH ID: 28979 Software Authors: Price, M.N., Dehal, P.S., Arkin, A.P. Description: FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. FastTree is open-source software – you can download the code below. FastTree is more accurate than PhyML 3 with default settings, and much more accurate than the distance-matrix methods that are traditionally used for large alignments. FastTree uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992), WAG (Whelan & Goldman 2001), or LG (Le and Gascuel 2008) models of amino acid evolution. To account for the varying rates of evolution across sites, FastTree uses a single rate for each site (the ”CAT” approximation). To quickly estimate the reliability of each split in the tree, FastTree computes local support values with the Shimodaira-Hasegawa test (these are the same as PhyML 3’s ”SH-like local supports”). Homepage: http://microbesonline.org/fasttree/ Related Software: ASTRAL-II; RAxML; BEAST; MLTreeMap; SEPP; Scoredist; pplacer; Quartets MaxCut; Seq-Gen; iGTP; PAUP*; BIONJ; BEAGLE; DEPP; PhyloGeoTool; INSTRAL; UShER; HmmUFOtu; TIPP; STEM-hy Cited in: 10 Publications all top 5 Cited by 17 Authors 3 Warnow, Tandy J. 2 Brown, Daniel G. 2 Kubatko, Laura Salter 2 Richards, Andrew 2 Truszkowski, Jakub 1 Balaban, Metin 1 Bayzid, Md. Shamsuzzoha 1 Biswas, Avijit 1 Desper, Richard 1 Gascuel, Olivier 1 Lin, Yu 1 Mirarab, Siavash 1 Moret, Bernard M. E. 1 Navid, Bin Hasan 1 Roddur, Mrinmoy Saha 1 Tang, Jijun 1 Willson, James K. Cited in 4 Serials 1 Bulletin of Mathematical Biology 1 Theoretical Computer Science 1 Computational Biology 1 Journal of Theoretical Biology Cited in 4 Fields 10 Biology and other natural sciences (92-XX) 2 Computer science (68-XX) 1 General and overarching topics; collections (00-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year