Piñeiro César, Pichel Juan C
Information Retrieval Lab, CITIC, Universidade da Coruña, A Coruña 15008, Spain.
CiTIUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae055.
Phylogenies play a crucial role in biological research. Unfortunately, the search for the optimal phylogenetic tree incurs significant computational costs, and most of the existing state-of-the-art tools cannot deal with extremely large datasets in reasonable times.
In this work, we introduce the new VeryFastTree code (version 4.0), which is able to construct a tree on 1 server using single-precision arithmetic from a massive 1 million alignment dataset in only 36 hours, which is 3 times and 3.2 times faster than its previous version and FastTree-2, respectively. This new version further boosts performance by parallelizing all tree traversal operations during the tree construction process, including subtree pruning and regrafting moves. Additionally, it introduces significant new features such as support for new and compressed file formats, enhanced compatibility across a broader range of operating systems, and the integration of disk computing functionality. The latter feature is particularly advantageous for users without access to high-end servers, as it allows them to manage very large datasets, albeit with an increase in computing time.
Experimental results establish VeryFastTree as the fastest tool in the state-of-the-art for maximum likelihood phylogeny estimation. It is publicly available at https://github.com/citiususc/veryfasttree. In addition, VeryFastTree is included as a package in Bioconda, MacPorts, and all Debian-based Linux distributions.
系统发育树在生物学研究中起着至关重要的作用。不幸的是，寻找最优系统发育树会产生巨大的计算成本，并且大多数现有的先进工具无法在合理时间内处理极其庞大的数据集。
在这项工作中，我们引入了新的VeryFastTree代码（版本4.0），它能够在1台服务器上使用单精度算法，仅用36小时就从100万个比对数据的海量数据集中构建一棵树，分别比其先前版本和FastTree - 2快3倍和3.2倍。这个新版本通过在树构建过程中并行化所有树遍历操作（包括子树剪枝和重新嫁接移动）进一步提高了性能。此外，它还引入了重要的新特性，如支持新的和压缩文件格式、增强在更广泛操作系统上的兼容性以及集成磁盘计算功能。后一个特性对无法使用高端服务器的用户特别有利，因为它允许他们管理非常大的数据集，尽管计算时间会增加。
实验结果表明VeryFastTree是用于最大似然系统发育估计的最先进工具中最快的工具。它可在https://github.com/citiususc/veryfasttree上公开获取。此外，VeryFastTree作为一个包包含在Bioconda、MacPorts和所有基于Debian的Linux发行版中。
