fasttree1
Create phylogenetic trees from alignments of nucleotide or protein sequences
Usage
fasttree protein_alignment
>
tree
fasttree -nt
nucleotide_alignment
>
tree
fasttree -nt
-gtr
<
nucleotide_alignment
>
tree
fasttree accepts
alignments
in
fasta
or
phylip
interleaved
formats
Detailed usage for fasttree 2.1.4 SSE3:
fasttree [-nt]
[-n
100]
[-quote]
[{-pseudo | -pseudo
1.0}]
or
fasttree [-nt]
[{-matrix
Matrix | -nomatrix}]
[-rawdist]
-makematrix
[alignment]
Constrained topology search options:
fasttree accepts
alignments
in
fasta
or
phylip
interleaved
formats
Overview
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.
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").
Releases
Unchanged in 7 releases since Debian 7 (Wheezy).