fasttree(1) | User Commands | fasttree(1) |
fasttree - create 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.
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").
fasttree protein_alignment > tree
fasttree -nt nucleotide_alignment > tree
fasttree -nt -gtr < nucleotide_alignment > tree
fasttree accepts alignments in fasta or phylip interleaved formats
-quiet to suppress reporting information
-nopr to suppress progress indicator
-log logfile -- save intermediate trees, settings, and model details
-fastest -- speed up the neighbor joining phase & reduce memory usage
-n <number> to analyze multiple alignments (phylip format only)
-nosupport to not compute support values
-intree newick_file to set the starting tree(s)
-intree1 newick_file to use this starting tree for all the alignments
-pseudo to use pseudocounts (recommended for highly gapped sequences)
-gtr -- generalized time-reversible model (nucleotide alignments only)
-wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)
-quote -- allow spaces and other restricted characters (but not ' characters) in
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
-gamma -- after optimizing the tree under the CAT approximation,
-constraints constraintAlignment to constrain the topology search
-expert -- see more options
fasttree [-nt] [-n 100] [-quote] [-pseudo | -pseudo 1.0]
or
fasttree [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment]
-n -- read in multiple alignments in. This only
-intree newickfile -- read the starting tree in from newickfile.
-intree with -n will read a separate starting tree for each alignment.
-intree1 newickfile -- read the same starting tree for each alignment
-quiet -- do not write to standard error during normal operation (no progress
-nopr -- do not write the progress indicator to stderr
-log logfile -- save intermediate trees so you can extract
-quote -- quote sequence names in the output and allow spaces, commas,
-pseudo [weight] -- Use pseudocounts to estimate distances between
-wag -- Whelan-And-Goldman 2001 model instead of (default) Jones-Taylor-Thorton 1992 model (a.a. only)
-gtr -- generalized time-reversible instead of (default) Jukes-Cantor (nt only)
-cat # -- specify the number of rate categories of sites (default 20)
-nocat -- no CAT model (just 1 category)
-gamma -- after the final round of optimizing branch lengths with the CAT model,
-slow -- exhaustive search (like NJ or BIONJ, but different gap handling)
-slow takes half an hour instead of 8 seconds for 1,250 proteins
-fastest -- search the visible set (the top hit for each node) only
-topm 1.0 -- set the top-hit list size to parameter*sqrt(N)
-close 0.75 -- modify the close heuristic, lower is more conservative
-refresh 0.8 -- compare a joined node to all other nodes if its
-2nd or -no2nd to turn 2nd-level top hits heuristic on or off
-nj: regular (unweighted) neighbor-joining (default)
-bionj: weighted joins as in BIONJ
-constraints alignmentfile -- an alignment with values of 0, 1, and -
-constraintWeight -- how strongly to weight the constraints. A value of 1
For more information, see http://www.microbesonline.org/fasttree/
fasttree accepts alignments in fasta or phylip interleaved formats
-quiet to suppress reporting information
-nopr to suppress progress indicator
-log logfile -- save intermediate trees, settings, and model details
-fastest -- speed up the neighbor joining phase & reduce memory usage
-n <number> to analyze multiple alignments (phylip format only)
-nosupport to not compute support values
-intree newick_file to set the starting tree(s)
-intree1 newick_file to use this starting tree for all the alignments
-pseudo to use pseudocounts (recommended for highly gapped sequences)
-gtr -- generalized time-reversible model (nucleotide alignments only)
-wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)
-quote -- allow spaces and other restricted characters (but not ' characters) in
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
-gamma -- after optimizing the tree under the CAT approximation,
-constraints constraintAlignment to constrain the topology search
-expert -- see more options
For more information, see http://www.microbesonline.org/fasttree/
June 2012 | Lawrence Berkeley National Lab |