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Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.
- Source :
- Bioinformatics; Sep2020, Vol. 36 Issue 17, p4658-4659, 2p
- Publication Year :
- 2020
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 36
- Issue :
- 17
- Database :
- Complementary Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 147074786
- Full Text :
- https://doi.org/10.1093/bioinformatics/btaa582