ASTRAL-Pro 2：从多拷贝基因家族树重建超快种系发生树。
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees.
机构信息
Bioinformatics and Systems Biology, UC San Diego, La Jolla, CA 92093, USA.
Department of Electrical and Computer Engineering, UC San Diego, La Jolla, CA 92093, USA.
出版信息
Bioinformatics. 2022 Oct 31;38(21):4949-4950. doi: 10.1093/bioinformatics/btac620.
MOTIVATION
Species tree inference from multi-copy gene trees has long been a challenge in phylogenomics. The recent method ASTRAL-Pro has made strides by enabling multi-copy gene family trees as input and has been quickly adopted. Yet, its scalability, especially memory usage, needs to improve to accommodate the ever-growing dataset size.
RESULTS
We present ASTRAL-Pro 2, an ultrafast and memory efficient version of ASTRAL-Pro that adopts a placement-based optimization algorithm for significantly better scalability without sacrificing accuracy.
AVAILABILITY AND IMPLEMENTATION
The source code and binary files are publicly available at https://github.com/chaoszhang/ASTER; data are available at https://github.com/chaoszhang/A-Pro2_data.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
从多拷贝基因树推断物种树一直是系统基因组学中的一个挑战。最近的方法 ASTRAL-Pro 通过允许多拷贝基因家族树作为输入取得了进展，并已被迅速采用。然而，它的可扩展性，特别是内存使用，需要改进以适应不断增长的数据集大小。
结果
我们提出了 ASTRAL-Pro 2，这是 ASTRAL-Pro 的一个超快速和内存高效版本，它采用了基于放置的优化算法，在不牺牲准确性的情况下显著提高了可扩展性。
可用性和实现
源代码和二进制文件可在 https://github.com/chaoszhang/ASTER 上公开获得；数据可在 https://github.com/chaoszhang/A-Pro2_data 上获得。
补充信息
补充数据可在 Bioinformatics 在线获得。
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