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.

To load this software in a Linux environment run the commands:

module load fasttree

To infer a tree for a protein alignment with the JTT+CAT model, use

FastTree < alignment_file > tree_file


FastTree alignment.file > tree_file

To infer a tree for a nucleotide alignment with the GTR+CAT model, use

FastTree -gtr -nt < alignment.file > tree_file


FastTree -gtr -nt alignment_file > tree_file

More documentation can be found here

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