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FASTTREE (version 2.1.10+galaxy1)
This tool is only available for fasta input only; FastTree will not be able to read these trees back in.
Specify if the aligned sequences are nucleotide or protein sequences


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. FastTree is open-source software.


  1. Aligned sequences file in FASTA format (e.g. the alignment from the 'PyNAST' tool) or PHYLIP format.
  2. Newick file to set the starting tree(s) (optional)


Nucleotide or protein alignment
To specify the type of sequence alignment (nucleotide or protein) you are providing.
Nucleotide evolution model
Specify GTR+CAT (Generalized Time Reversable Model) or Jukes-Cantor + CAT.
Protein evolution model
Specify JTT (Jones-Taylor-Thornton 1992 model) + CAT, WAG (Whelan-And-Goldman 2001 model) + CAT, or LG (Le-Gascuel 2008 model) + CAT.
Allow spaces and other restricted characters (but not ') in sequence and quote names in the output tree. (fasta only)
FastTree will not be able to read these trees back in. (-quote)
Number of multiple alignments (phylip only)

Advanced Parameters

Number of rates of sites
Defaults to 20. Specify whether you wish to choose constant rates. (-cat/-nocat)
Use Gamma20
After optimizing the tree under the CAT approximation, rescale the lengths to optimize the Gamma20 likelihood. (-gamma)
Eliminates the support value computation. Support value computation is not recommended for wide alignments.
Turn off maximum-likelihood.
Speed up the neighbor joining phase and reduce memory usage
Recommended for >50,000 sequences. (-fastest)
Use pseudocounts
Recommended if you have many fragmentary sequences. (-pseudo)
Optimize branch lengths without ML NNIs.


This tool produces two output files, one of which is optional (the log file).

  1. The phylogenetic tree in Newick format (nhx).
  2. (optional) The log file, containing information of the FastTree run to build the phylogenetic tree.

The placement of the root is not biologically meaningful. The local support values are given as names for the internal nodes, and range from 0 to 1, not from 0 to 100 or 0 to 1,000. If all sequences are unique, then the tree will be fully resolved (the root will have three children and other internal nodes will have two children). If there are multiple sequences that are identical to each other, then there will be a multifurcation. Also, there are no support values for the parent nodes of redundant sequences.