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PROGRAM:
NAME
fasttree - create phylogenetic trees from alignments of nucleotide or protein sequences
DESCRIPTION
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").
SYNOPSIS
fasttree protein_alignment > tree
fasttree -nt nucleotide_alignment > tree
fasttree -nt -gtr < nucleotide_alignment > tree
fasttree accepts alignments in fasta or phylip interleaved formats
Common options (must be before the alignment file):
-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
(recommended for >50,000 sequences)
-n <number> to analyze multiple alignments (phylip format only)
(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
-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
(for faster global bootstrap on huge 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
sequence names and quote names in the output tree (fasta input only; fasttree will
not be able to read these trees back in
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
(recommended if running additional ML NNIs with -intree)
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
or -nocat to use constant rates
-gamma -- after optimizing the tree under the CAT approximation,
rescale the lengths to optimize the Gamma20 likelihood
-constraints constraintAlignment to constrain the topology search
constraintAlignment should have 1s or 0s to indicates splits
-expert -- see more options
Detailed usage for fasttree 2.1.4 SSE3:
fasttree [-nt] [-n 100] [-quote] [-pseudo | -pseudo 1.0]
[-boot 1000 | -nosupport] [-intree starting_trees_file | -intree1
starting_tree_file] [-quiet | -nopr] [-nni 10] [-spr 2] [-noml | -mllen | -mlnni
10] [-mlacc 2] [-cat 20 | -nocat] [-gamma] [-slow | -fastest] [-2nd | -no2nd]
[-slownni] [-seed 1253] [-top | -notop] [-topm 1.0 [-close 0.75] [-refresh 0.8]]
[-matrix Matrix | -nomatrix] [-nj | -bionj] [-wag] [-nt] [-gtr] [-gtrrates ac ag at
cg ct gt] [-gtrfreq A C G T] [ -constraints constraintAlignment [ -constraintWeight
100.0 ] ] [-log logfile]
[ alignment_file ]
> newick_tree
or
fasttree [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment]
[-n 100] > phylip_distance_matrix
fasttree supports fasta or phylip interleaved alignments By default fasttree
expects protein alignments, use -nt for nucleotides fasttree reads standard input
if no alignment file is given
Input/output options:
-n -- read in multiple alignments in. This only
works with phylip interleaved format. For example, you can use it with the output
from phylip's seqboot. If you use -n, fasttree will write 1 tree per line to
standard output.
-intree newickfile -- read the starting tree in from newickfile.
Any branch lengths in the starting trees are ignored.
-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
indicator, no options summary, no likelihood values, etc.)
-nopr -- do not write the progress indicator to stderr
-log logfile -- save intermediate trees so you can extract
the trees and restart long-running jobs if they crash -log also reports the
per-site rates (1 means slowest category)
-quote -- quote sequence names in the output and allow spaces, commas,
parentheses, and colons in them but not ' characters (fasta files only)
Distances:
Default: For protein sequences, log-corrected distances and an
amino acid dissimilarity matrix derived from BLOSUM45
or for nucleotide sequences, Jukes-Cantor distances To specify a different matrix,
use -matrix FilePrefix or -nomatrix Use -rawdist to turn the log-correction off or
to use %different instead of Jukes-Cantor
-pseudo [weight] -- Use pseudocounts to estimate distances between
sequences with little or no overlap. (Off by default.) Recommended if analyzing the
alignment has sequences with little or no overlap. If the weight is not specified,
it is 1.0
Topology refinement:
By default, fasttree tries to improve the tree with up to 4*log2(N) rounds of
minimum-evolution nearest-neighbor interchanges (NNI), where N is the number of
unique sequences, 2 rounds of subtree-prune-regraft (SPR) moves (also min. evo.),
and up to 2*log(N) rounds of maximum-likelihood NNIs. Use -nni to set the number
of rounds of min. evo. NNIs, and -spr to set the rounds of SPRs. Use -noml to turn
off both min-evo NNIs and SPRs (useful if refining
an approximately maximum-likelihood tree with further NNIs)
Use -sprlength set the maximum length of a SPR move (default 10) Use -mlnni to set
the number of rounds of maximum-likelihood NNIs Use -mlacc 2 or -mlacc 3 to always
optimize all 5 branches at each NNI,
and to optimize all 5 branches in 2 or 3 rounds
Use -mllen to optimize branch lengths without ML NNIs Use -mllen -nome with -intree
to optimize branch lengths on a fixed topology Use -slownni to turn off heuristics
to avoid constant subtrees (affects both
ML and ME NNIs)
Maximum likelihood model options:
-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,
report the likelihood under the discrete gamma model with the same number of
categories. fasttree uses the same branch lengths but optimizes the gamma shape
parameter and the scale of the lengths. The final tree will have rescaled lengths.
Used with -log, this also generates per-site likelihoods for use with CONSEL, see
GammaLogToPaup.pl and documentation on the fasttree web site.
Support value options:
By default, fasttree computes local support values by resampling the site
likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify -nome, it
will compute minimum-evolution bootstrap supports instead In either case, the
support values are proportions ranging from 0 to 1
Use -nosupport to turn off support values or -boot 100 to use just 100 resamples
Use -seed to initialize the random number generator
Searching for the best join:
By default, fasttree combines the 'visible set' of fast neighbor-joining with
local hill-climbing as in relaxed neighbor-joining
-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
Unlike the original fast neighbor-joining, -fastest updates visible(C) after
joining A and B if join(AB,C) is better than join(C,visible(C)) -fastest also
updates out-distances in a very lazy way, -fastest sets -2nd on as well, use
-fastest -no2nd to avoid this
Top-hit heuristics:
By default, fasttree uses a top-hit list to speed up search Use -notop (or -slow)
to turn this feature off
and compare all leaves to each other, and all new joined nodes to each other
-topm 1.0 -- set the top-hit list size to parameter*sqrt(N)
fasttree estimates the top m hits of a leaf from the top 2*m hits of a 'close'
neighbor, where close is defined as d(seed,close) < 0.75 * d(seed, hit of rank
2*m), and updates the top-hits as joins proceed
-close 0.75 -- modify the close heuristic, lower is more conservative
-refresh 0.8 -- compare a joined node to all other nodes if its
top-hit list is less than 80% of the desired length, or if the age of the top-hit
list is log2(m) or greater
-2nd or -no2nd to turn 2nd-level top hits heuristic on or off
This reduces memory usage and running time but may lead to marginal reductions in
tree quality. (By default, -fastest turns on -2nd.)
Join options:
-nj: regular (unweighted) neighbor-joining (default)
-bionj: weighted joins as in BIONJ
fasttree will also weight joins during NNIs
Constrained topology search options:
-constraints alignmentfile -- an alignment with values of 0, 1, and -
Not all sequences need be present. A column of 0s and 1s defines a constrained
split. Some constraints may be violated (see 'violating constraints:' in standard
error).
-constraintWeight -- how strongly to weight the constraints. A value of 1
means a penalty of 1 in tree length for violating a constraint Default: 100.0
For more information, see http://www.microbesonline.org/fasttree/
or the comments in the source code
fasttree protein_alignment > tree fasttree -nt nucleotide_alignment > tree fasttree
-nt -gtr < nucleotide_alignment > tree
fasttree accepts alignments in fasta or phylip interleaved formats
Common options (must be before the alignment file):
-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
(recommended for >50,000 sequences)
-n <number> to analyze multiple alignments (phylip format only)
(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
-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
(for faster global bootstrap on huge 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
sequence names and quote names in the output tree (fasta input only; fasttree will
not be able to read these trees back in
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
(recommended if running additional ML NNIs with -intree)
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
or -nocat to use constant rates
-gamma -- after optimizing the tree under the CAT approximation,
rescale the lengths to optimize the Gamma20 likelihood
-constraints constraintAlignment to constrain the topology search
constraintAlignment should have 1s or 0s to indicates splits
-expert -- see more options
For more information, see http://www.microbesonline.org/fasttree/
Use fasttree online using onworks.net services
