Phylogenetic trees analysis made easy. 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. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7.

First, FastTree uses a heuristic variant of neighbor joining to get a rough topology. During neighbor joining, FastTree stores profiles of internal nodes instead of a distance matrix, which reduces the memory required. FastTree uses a combination of three heuristics to speed up this phase: it remembers the best join for each node, as in fast neighbor-joining; it does a hill-climbing search for better joins from a candidate join, as in relaxed neighbor joining; and it uses the "top hits" heuristic to avoid computing all pairwise distances and to avoid considering all possible joins at every step. It also updates the best join for a node as it comes across them, which reduces the amount of hill-climbing. Another limitation of FastTree's neighbor-joining phase is that it does not correct the distances for multiple substitutions, which exacerbates long-branch attraction. However, this will be corrected in the next stage.

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