Maddison Wayne P
Beaty Biodiversity Museum and Departments of Zoology and Botany, University of British Columbia, Vancouver, British Columbia, Canada.
PeerJ. 2024 Dec 5;12:e18504. doi: 10.7717/peerj.18504. eCollection 2024.
In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.
在系统发育基因组学中，比对可靠性低且噪声高的区域通常会在用于系统发育推断之前从多序列比对中去除。我引入了一种新的去除工具PhyIN，它会删除大部分位点（字符）具有冲突系统发育信号的区域。它不需要推断系统发育树，因为它会找到在任何可能的树上都无法达成一致的相邻字符。在超保守元件（UCE）的系统发育基因组数据中，PhyIN仅使用单个位点的数据就能有效地找到比对中混乱（冲突）区域和有序区域之间的边界。它在单个位点上工作的能力使其能够保留基因树和物种树之间的不一致性。
