968 citations
4 runs

FastTree

By Price M., Arkin A., Last update 1494698998
All tools Run this tool

FastTree description

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 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) or WAG (Whelan & Goldman 2001) 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').


Parent program: FastTree

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 uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT (Jones-Taylor-Thornton 1992) or WAG (Whelan & Goldman 2001) 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').