FastTree/en
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:
To load a single precision module:
To load a double precision module:
Troubleshooting¶
Warning: Closely-related and very long sequences
If you encounter the warning message "WARNING! This alignment consists of closely-related and very long sequences", this likely results in very short and sometimes negative branch lengths. To resolve this, use a fasttree-double module for double precision calculations.