2.2.0

Main tool: FastTree

Full documentation: http://www.microbesonline.org/fasttree/

Usage

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

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/