UFBoot2：改进超快bootstrap 逼近算法。
UFBoot2: Improving the Ultrafast Bootstrap Approximation.
机构信息
Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University Vienna, Vienna, Austria.
出版信息
Mol Biol Evol. 2018 Feb 1;35(2):518-522. doi: 10.1093/molbev/msx281.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
标准自举法（SBS）尽管计算量很大，但在最大似然系统发育分析中被广泛应用。我们最近提出了超快自举逼近法（UFBoot），在轻度违反模型的情况下，与 SBS 相比，UFBoot 可以减少计算时间，同时获得更无偏的分支支持。UFBoot 已逐渐被用作 SBS 和其他自举方法的有效替代方法。在这里，我们提出了 UFBoot2，它大大加快了 UFBoot 的速度，并降低了由于多系或严重违反模型而高估分支支持的风险。此外，UFBoot2 为基因组数据提供了合适的自举重采样策略。在测试数据集上，UFBoot2 比 SBS 快 778 倍（中位数），比 RAxML 快速自举快 8.4 倍（中位数）。UFBoot2 是在 IQ-TREE 软件包版本 1.6 中实现的，并可在 http://www.iqtree.org 上免费获得。
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