FastTree

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):

(recommended for >50,000 sequences)

(use for global bootstrap, with seqboot and CompareToBootstrap.pl)

(for faster global bootstrap on huge alignments)

sequence names and quote names in the output tree (fasta input only; fasttree will not be able to read these trees back in

(recommended if running additional ML NNIs with -intree)

or -nocat to use constant rates

rescale the lengths to optimize the Gamma20 likelihood

constraintAlignment should have 1s or 0s to indicates splits

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:

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.

Any branch lengths in the starting trees are ignored.

indicator, no options summary, no likelihood values, etc.)

the trees and restart long-running jobs if they crash -log also reports the per-site rates (1 means slowest category)

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

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:

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

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

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

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

This reduces memory usage and running time but may lead to marginal reductions in tree quality. (By default, -fastest turns on -2nd.)

Join options:

fasttree will also weight joins during NNIs

Constrained topology search options:

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).

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):

(recommended for >50,000 sequences)

(use for global bootstrap, with seqboot and CompareToBootstrap.pl)

(for faster global bootstrap on huge alignments)

sequence names and quote names in the output tree (fasta input only; fasttree will not be able to read these trees back in

(recommended if running additional ML NNIs with -intree)

or -nocat to use constant rates

rescale the lengths to optimize the Gamma20 likelihood

constraintAlignment should have 1s or 0s to indicates splits

For more information, see http://www.microbesonline.org/fasttree/