FastTree

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million sequences in a reasonable amount of time and memory.

Environment modules

We offer software modules for single precision and double precision calculations. Single precision is faster while double precision is more precise. Double precision is recommended when using a highly biased transition matrix, or if you want to resolve very short branches accurately.

To see the available FastTree modules:

module spider fasttree

To load a single precision module:

module load fasttree/2.1.11

To load a double precision module:

module load fasttree-double/2.1.11

Troubleshooting

• Error message WARNING! This alignment consists of closely-related and very long sequences: This likely results in very short and sometimes negative branch lengths. Use a fasttree-double module for double precision.

References

• https://morgannprice.github.io/fasttree/ FastTree Web page]