Provided by: veryfasttree_4.0.3+dfsg-1_amd64 
NAME
VeryFastTree - Speeding up the estimation of phylogenetic trees for large alignments
through parallelization and vectorization strategies
DESCRIPTION
VeryFastTree is a highly efficient implementation inspired by the FastTree-2 tool,
designed to expedite the inference of approximately-maximum-likelihood phylogenetic trees
from nucleotide or protein sequence alignments. It is an optimized implementation designed
to accelerate the estimation of phylogenies for large alignments. By leveraging
parallelization and vectorization strategies, VeryFastTree significantly improves the
performance and scalability of phylogenetic analysis, allowing it to construct
phylogenetic trees in a fraction of the time previously required.
Maintaining the integrity of FastTree-2, VeryFastTree retains the same phases, methods,
and heuristics used for estimating phylogenetic trees. This ensures that the topological
accuracy of the trees produced by VeryFastTree remains equivalent to that of FastTree-2.
Moreover, unlike the parallel version of FastTree-2, VeryFastTree guarantees deterministic
results, eliminating any potential variations in the output.
To facilitate a seamless transition for users, VeryFastTree adopts the exact same command
line arguments as FastTree-2. This means that by simply substituting FastTree-2 with
VeryFastTree, and using the same set of options, users can significantly enhance the
overall performance of their phylogenetic analyses.
VeryFastTree 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.
VeryFastTree 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, VeryFastTree uses a
single rate for each site (the "CAT" approximation). To quickly estimate the reliability
of each split in the tree, VeryFastTree computes local support values with the Shimodaira-
Hasegawa test (these are the same as PhyML 3's "SH-like local supports").
SYNOPSIS
VeryFastTree protein_alignment > tree
VeryFastTree -nt nucleotide_alignment > tree
VeryFastTree -nt -gtr < nucleotide_alignment > tree
accepts alignments in NEXUS, Fasta, Fastq or Phylip interleaved formats compressed with
ZLib and libBZ2.
Common options:
-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)
sequence names and quote names in the output tree (fasta input only; VeryFastTree 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 -threads <number> (Env:OMP_NUM_THREADS)
number of threads (n) used in the parallel execution
-double-precision -- to use double precision arithmetic. Therefore, it is equivalent to
compile FastTree-2 with -DUSE_DOUBLE.
-ext name to speed up computations enabling the vector extensions. Available:
AUTO(default), NONE, SSE, SSE3 , AVX, AVX2, AVX512 or CUDA
-expert -- see more options
Detailed usage for VeryFastTree:
VeryFastTree [-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]] [-gtr] [-gtrrates ac ag at cg ct gt] [-gtrfreq A C G T] [ -lg | -wag |
-trans transitionmatrixfile ] [-matrix Matrix | -nomatrix] [-nj | -bionj] [ -constraints
constraintAlignment [ -constraintWeight 100.0 ] ] [-log logfile] [ alignment_file ] [
-threads 1 ] [ -threads-level 3 [ -threads-ptw 20 ] [-threads-verbose] [ -double-precision
] [ -ext AUTO ] [ -fastexp 0 ] [ -disk-computing ] [ -disk-computing-path ./ ] [
-disk-dynamic-limit inf ] [ -relative-progress ] [ -out output_newick_file | >
newick_tree]
or
VeryFastTree [-nt] [-matrix Matrix | -nomatrix] [-rawdist] -makematrix [alignment] [-n
100] > phylip_distance_matrix
VeryFastTree supports NEXUS, Fasta, Fastq or Phylip interleaved formats
VeryFastTree supports files compressed with ZLib and libBZ2
By default VeryFastTree expects protein alignments, use -nt for nucleotides
VeryFastTree reads standard input if no alignment file is given
Input/output options:
-out file print tree in output file instead of stdout
-n <number> 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, VeryFastTree will write 1 tree per line to standard output.
-nt -- nucleotides instead of protein alignments
-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
-verbose lvl level of details during normal operation
-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 (These options affect minimum-evolution computations only; use -trans to
affect maximum-likelihoood computations)
-makematrix -- print distance matrix
-rawdist -- to turn the log-correction off
-matrix file to turn the log-correction off
-nomatrix -- to turn the log-correction off
-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, VeryFastTree 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.
-nni <number> to set the number of rounds of min. evo. NNIs
-spr <number> to set the rounds of SPRs
-noml -- to turn off both min-evo NNIs and SPRs (useful if refining an approximately
maximum-likelihood tree with further NNIs)
-sprlength <number> set the maximum length of a SPR move (default 10)
-mlnni <number> to set the number of rounds of maximum-likelihood NNIs
-mlacc <number> 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
-mllen -- to optimize branch lengths without ML NNIs. Use -mllen -nome with -intree to
optimize branch lengths on a fixed topology
-approxml,-mlapprox -- approximate posterior distributions for a.a.s
-slownni -- to optimize branch lengths without ML NNIs.
Maximum likelihood model options:
-lg -- Le-Gascuel 2008 model instead of (default) Jones-Taylor-Thorton 1992 model (a.a.
only)
-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)
-gtrrates rates set the gtr rates
-gtrfreq seqs set the gtr frequences
-cat # -- specify the number of rate categories of sites (default 20)
-nocat -- no CAT model (just 1 category)
-trans filename use the transition matrix from filename.This is supported for amino acid
alignments only.The file must be tab-delimited with columns in the order
ARNDCQEGHILKMFPSTWYV*.The additional column named * is for the stationary
distribution.Each row must have a row name in the same order ARNDCQEGHILKMFPSTWYV
-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.
VeryFastTree 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 VeryFastTree web site.
Support value options:
By default, VeryFastTree 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
-nome -- to compute minimum-evolution bootstrap supports
-nosupport -- to turn off support values
-boot <number> to use just n resamples
-noboot -- to no use resamples
-seed <number> to initialize the random number generator
Searching for the best join:
By default, VeryFastTree 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, VeryFastTree uses a top-hit list to speed up search
-top 0.01 set the top-hit list size to 1.0 if it is less than 0.01 -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) VeryFastTree 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 VeryFastTree 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 w 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
Optimizations:
-threads <number> (Env:OMP_NUM_THREADS) number of threads used in the parallel execution.
If this option is not set, the corresponding value will be obtained from the
environment variable OMP_NUM_THREADS. This is the same approach followed by
FastTree-2. If n=1, VeryFastTree behaves in the same way than FastTree-2 compiled
without the -DOPENMP flag
-threads-level <number> in [0 - 4] degree of parallelization. If level is 0, VeryFastTree
uses the same parallelization strategy as FastTree-2 with some new parallel blocks.
If level is 1, VeryFastTree uses parallel blocks that require additional memory for
computation. If level is 2, VeryFastTree accelerates the rounds of ML NNIs using
its tree partitioning method. If level is 3 (default), VeryFastTree performs more
computations without preserving sequential order. If level is 4, VeryFastTree
accelerates the rounds of SPR steps using its tree partitioning method (it can only
be used with datasets larger than 2^sprlength + 2).
Note: Each level includes the previous ones, and computation at level 2 and above is
performed in a different tree traverse order, so the result may change but is still
correct
-threads-mode <number> in [0 - 1] changes the mode of parallelization. If level is 0,
VeryFastTree uses non-deterministic parts, some inspired by FastTree-2 but
improved. If level is 1 (default), VeryFastTree only uses deterministic
parallelization. Since version 4.0, deterministic algorithms are at least faster
than non-deterministic ones, making deterministic the preferred choice
-threads-ptw <number> (Partitioning Tendency Window) It sets the size of the partitioning
tendency window used by the tree partitioning algorithm to determine when to stop
searching. The window stores the last solutions and checks if a better solution can
be found. Increasing the value allows the algorithm to explore the tree deeper and
potentially find better solutions. The default value is 20.
-threads-verbose -- to show subtrees assigned to the threads and theoretical
speedup, only with verbose > 0
-double-precision -- to use double precision arithmetic. Therefore, it is equivalent to
compile FastTree-2 with -DUSE_DOUBLE
-ext name to speed up computations enabling the vector extensions. Available:
AUTO(default), NONE, SSE, SSE3 , AVX, AVX2, AVX512 or CUDA
-fastexp <number> in [0 - 3] to select an alternative implementation for the exponential
function exp(x), which has a significant impact on performance. Options: 0 -
built-in math library with double precision (default), 1 - built-in math library
with simple precision (not recommended with -double-precision option), 2 - fast
implementation to compute an approximation of exp(x) using double precision, and 3
- fast implementation to compute an approximation of exp(x) using simple precision
(not recommended with -double-precision option)
-disk-computing -- if there is not enough available RAM to perform the computation, disk
will be used to store extra data when it was not needed. Using disk to perform the
computation will substantially increase the execution time
-disk-computing-path path like -disk-computing but using a custom path folder to store
data
-disk-dynamic-computing -- by default, disk computing only creates files associated with
static data in RAM, which means that there is no significant impact on performance
as long as there is available RAM. This option further reduces memory usage by
storing dynamic data on disk. However, even if there is enough RAM, it will have a
negative impact on performance due to the constant creation and deletion of files
-disk-dynamic-limit <number> -disk-dynamic-computing can exceed the limit of memory-mapped
file system. If 'memory mapping fails' errors occur, setting a limit will solve the
problem. In Linux, the limit can be checked with 'sysctl vm.max_map_count'. It is
important not to use the exact value and leave a small margin for other operations
that require this feature
-relative-progress -- to shows relative time to previous step rather than absolute time in
progress report
Deprecated:
-logdist -- use logarithmic distances, now on by default and obsolete
-exactml -- Exact posterior distributions, now on by default and obsolete
-mlexact -- Exact posterior distributions, now on by default and obsolete
For more information, see https://github.com/citiususc/veryfasttree or
http://www.microbesonline.org/fasttree/