Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations
复制标题
具有反复突变的 SARS-CoV-2 系统发育的可扩展重建
DOI：
10.1089/cmb.2021.0306
复制
发表时间：
2021
影响因子：
1.7
通讯作者：
Zelikovsky, Alex
中科院分区：
文献类型：
--
作者：
Novikov, Daniel;Knyazev, Sergey;Grinshpon, Mark;Icer, Pelin;Skums, Pavel;Zelikovsky, Alex
本文提出了一种新的用于密集病毒测序数据的可扩展的基于特征的系统发生算法，称为SPHERE(具有重复突变的可扩展系统发生)。该算法基于一个进化模型，在该模型中，允许重复突变，但禁止反向突变。该算法创建了有根的基于特征的系统发育树，其中所有的叶子和内部节点都用观察到的类群来标记。我们表明，球体的系统发育比NextStress的更稳定，而且它准确地推断了从早期大流行到已知的传播联系。Sphere是一种快速算法，可以在<；2小时内处理>；200,000个序列，它提供了全球共享所有流感数据倡议(GISAID)的紧凑系统发育可视化。
This article presents a novel scalable character-based phylogeny algorithm for dense viral sequencing data called SPHERE (Scalable PHylogEny with REcurrent mutations). The algorithm is based on an evolutionary model where recurrent mutations are allowed, but backward mutations are prohibited. The algorithm creates rooted character-based phylogeny trees, wherein all leaves and internal nodes are labeled by observed taxa. We show that SPHERE phylogeny is more stable than Nextstrain's, and that it accurately infers known transmission links from the early pandemic. SPHERE is a fast algorithm that can process >200,000 sequences in <2 hours, which offers a compact phylogenetic visualization of Global Initiative on Sharing All Influenza Data (GISAID).
影响因子：
5.8
作者：
Sand, Andreas;Holt, Morten K.;Pedersen, Christian N. S.
通讯作者：
Pedersen, Christian N. S.