VeryFastTree1
Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies
Usage
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:
sequence names
and
quote
names
in
the
output
tree
(fasta
input
only;
VeryFastTree
will
not
be
able
to
read
these
trees
back
in
Detailed usage for VeryFastTree:
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
VeryFastTree reads
standard
input
if
no
alignment
file
is
given
Overview
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").