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

• Published in: Bioinformatics Vol. 36; no. 17; pp. 4658 - 4659
• Main Authors: Piñeiro, César, Abuín, José M, Pichel, Juan C
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.11.2020
• Subjects: Algorithms; Computers; Phylogeny; Sequence Alignment; Software; Trees
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btaa582

Abstract 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.