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Updated: Dec 17, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and
César Piñeiro1, José M Abuín1, Juan C Pichel1
1Centro de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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.
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