VeryFastTree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies

TítuloVeryFastTree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies
AutoresCésar Piñeiro, José M. Abuín and Juan C. Pichel
TipoArtículo de revista
Fonte Bioinformatics, Oxford University Press, 2020.
RankProvisionally ranked Q1 in Biochemistry by SJR 2019
ISSN1367-4803
DOI10.1093/bioinformatics/btaa582
AbstractMotivation: 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