FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
FastTree infers approximately-maximum-likelihood phylogenetic trees from
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory. For
large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.
Location and version:
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$ which FastTree
/local/cluster/bin/FastTree
$ which FastTreeMP
/local/cluster/bin/FastTreeMP
$ which FastTreeDbl
/local/cluster/bin/FastTreeDbl
$ FastTree -expert
Detailed usage for FastTree 2.1.11 SSE3:
...
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help message:
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$ FastTree -help
FastTree 2.1.11 SSE3:
FastTree protein_alignment > tree
FastTree < protein_alignment > tree
FastTree -out tree protein_alignment
FastTree -nt nucleotide_alignment > tree
FastTree -nt -gtr < nucleotide_alignment > tree
FastTree < 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)
-lg -- Le-Gascuel 2008 model (amino acid alignments only)
-wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)
-quote -- allow spaces and other restricted characters (but not ' ) 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/
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To control the number of threads to use with the FastTreeMP version:
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export OMP_NUM_THREADS=<THREADS> # bash
setenv OMP_NUM_THREADS <THREADS> # tcsh
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I suggest using the -gtr flag for nucleotide alignments and the -lg flag for
amino acid alignments for best accuracy if you’re not sure what model to choose.
software ref: http://www.microbesonline.org/fasttree
research ref: https://doi.org/10.1371/journal.pone.0009490