Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.

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 h, which is 7.8× and 3.5× faster than the sequential and best parallel FastTree-2 times, respectively.

Availability And Implementation: VeryFastTree is available at the GitHub repository: https://github.com/citiususc/veryfasttree.

Supplementary Information: Supplementary data are available at Bioinformatics online.