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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

FastTree is available in our software modules. We offer modules for single- 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 check 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


  • WARNING! This alignment consists of closely-related and very-long sequences. Such an alignment will likely result in very short, sometimes even negative branch lengths. Use a fasttree-double module for double precision.