Main tool: FastTree v2.1.11 Full documentation: http://www.microbesonline.org/fasttree/
Docker container information:
This Docker container installs and runs FastTree using Ubuntu Bionic as a base image. No other dependencies are needed to run FastTree. The small sequence alignment (covid_alignment.fasta) also in the container is used to test the Docker build.
Usage for FastTree version 2.1.11
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.
FastTree accepts alignments in fasta or phylip interleaved formats
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
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)
-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
Example command-line input for basic FastTree phylogeny
FastTree -log fasttree_test_log -nt sample.fasta > fasttree_test.nwk
For more information, see http://www.microbesonline.org/fasttree/