PDF(Pubmed)
Abstract：
BACKGROUND: 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.
RESULTS: 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.
CONCLUSIONS: 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.
RESULTS: 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.
CONCLUSIONS: 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.
摘要：
背景：系统发育在生物学研究中起着至关重要的作用。不幸的是,寻找最优的系统发育树带来了巨大的计算成本，大多数现有的最先进的工具无法在合理的时间内处理非常大的数据集。
结果：在这项工作中，我们介绍了新的VeryFastTree代码（版本4.0），它能够在一台服务器上使用单精度算法在36小时内从一个庞大的100万个对齐数据集中构建一棵树，分别比以前的版本和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，进一步提高了性能。包括子树修剪和回归动作。此外,它引入了重要的新功能，例如支持新的和压缩的文件格式，在更广泛的操作系统中增强兼容性，以及磁盘计算功能的集成。后一个特征对于没有访问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，尽管计算时间增加了。
结论：实验结果证明VeryFastTree是最先进的最大似然系统发育估计工具中最快的工具。它可以在https://github.com/citiususec/veryfasttree上公开获得。此外,VeryFastTree作为包包含在Bioconda中，MacPorts,和所有基于Debian的Linux发行版。
结果：在这项工作中，我们介绍了新的VeryFastTree代码（版本4.0），它能够在一台服务器上使用单精度算法在36小时内从一个庞大的100万个对齐数据集中构建一棵树，分别比以前的版本和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，进一步提高了性能。包括子树修剪和回归动作。此外,它引入了重要的新功能，例如支持新的和压缩的文件格式，在更广泛的操作系统中增强兼容性，以及磁盘计算功能的集成。后一个特征对于没有访问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，尽管计算时间增加了。
结论：实验结果证明VeryFastTree是最先进的最大似然系统发育估计工具中最快的工具。它可以在https://github.com/citiususec/veryfasttree上公开获得。此外,VeryFastTree作为包包含在Bioconda中，MacPorts,和所有基于Debian的Linux发行版。
