Cipres Science Gateway | FastTree2 Information

FastTree2

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. According to the authors, FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory, and is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

FastTree is open source, and has home site. We refer users there for the most recent, and best information on use of this program.

Input files: FastTree accepts as input Protein or DNA matrices in aligned fasta or interleaved Phylip format. The user may also provide a starting or constraint tree in Newick format, and a splitconstraints alignment file. FastTree developers make the following recommendations for creating input files: use MUSCLE to create an alignment matrix, and use gblocks to "trim" it (remove low-confidence parts of the alignment, such as positions that contain many gaps). For large protein families, use hmmalign from the HMMer package. If using hmmalign, you should remove columns that do not match the model (usually output in lower case). For large RNA families they recommend Infernal.

FastTree has a restrictive alphabet for nucleotides ACGT (and U) and amino acids (ARNDCQEGHILKMFPSTWYV). Other characters (such as U for selenomethionine) are treated as missing data, a warning is issued. Thus, FastTree will report warnings for alignments that contain ambiguous 1-letter codes (R or N for nucleotides or Z or X for amino acids) or rare amino acids (e.g. U for selenomethionine). Missing data missing data or gaps shouild be represented as "-".

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names	Sample File from a Test
alignment file	fasttree_infile.phy
starting tree	fasttree_starting_tree.tre

Sample Output File Type	File Name
log file	fasttree_logfile.txt
tree file	fastree_result.tre

FastTree developers recommend MEGA for viewing small trees, Archaeopteryx for large trees, and Arb for huge trees.

If you use FASTTree here, please cite:

Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Molecular Biology and Evolution 26:1641-1650, doi:10.1093/molbev/msp077. Freely available at MBE.
Price, M.N., Dehal, P.S., and Arkin, A.P. (2010) FastTree 2 -- Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5(3):e9490. doi:10.1371/journal.pone.0009490.
Freely available at PLoS ONE.

If there is a tool or a feature you need, please let us know.