fasttreeMP

phylogenetic trees from alignments of nucleotide or protein sequences

Install

All systems
curl cmd.cat/fasttreeMP.sh
Debian Debian
apt-get install fasttree
Ubuntu
apt-get install fasttree
image/svg+xml Kali Linux
apt-get install fasttree
Windows (WSL2)
sudo apt-get update sudo apt-get install fasttree
Raspbian
apt-get install fasttree

fasttree

phylogenetic trees from alignments of nucleotide or protein sequences

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It handles 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) model 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"). This package contains a single threaded version (fasttree) and a parallel version which uses OpenMP (fasttreMP).