Motivation: FastTree-2 is one of the most successful tools for inferring large phylogenies. With speed at the core of its design, there are still important issues in the FastTree-2 implementation that harm its performance and scalability. To deal with these limitations we introduce VeryFastTree, a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to boost performance.
Results: VeryFastTree is able to construct a tree on a standard server using double precision arithmetic from an ultra-large 330k alignment in only 4.5 hours, which is 7.8× and 3.5× faster than the sequential and best parallel FastTree-2 times, respectively.
Availability: VeryFastTree is available at the GitHub repository: https://github.com/citiususc/veryfasttree