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.

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").