Pseudocounts for highly fragmentary sequences.
Shimodaira-Hasegawa test (these are the same as PhyML 3's "SH-like local supports"). To quickly estimate the reliability of each split in the tree, FastTree computes To account for the varying rates of evolution across sites,įastTree uses a single rate for each site (the "CAT" approximation). FastTree 2.1: Approximately-Maximum-Likelihood Trees for Large Alignments FastTreeįastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.įastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.įor large alignments, FastTree is 100-1,000 times faster thanįastTree is open-source software - you can download the code below.įastTree is more accurate than PhyML 3 with default settings,Īnd much more accurate than the distance-matrix methods that are traditionally usedįastTree 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.
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