A vector representation of phylogenetic trees

发布时间：2024-05-31 作者：浏览次数：

Speaker:	张洛欣	DateTime:	2024年6月12日(周三）下午2:30-3:30
Brief Introduction to Speaker: 张洛欣教授在加拿大滑铁卢大学获计算机博士学位，现为新加坡国立大学数学系教授、博士生导师。主要研究方向为计算生物学、离散应用数学和理论计算机科学，在生物序列进化分析理论和算法方面发表上百篇论文，2005年获国家自然科学基金委B类杰出青年基金，1997年获新加坡李光耀博士后研究奖。		Place:	M323
Abstract:Good representations for phylogenetic trees and networks are important for enhancing storage efficiency and scalability for the inference and analysis of evolutionary trees for genes, genomes and species. We propose a new representation for rooted phylogenetic trees that encodes a tree on n taxa as a vector of length 2n in which each taxon appears exactly twice. Using this new tree representation, we introduce a novel tree rearrangement operator, termed a HOP, that results in a tree space of diameter n and a quadratic neighbourhood size. We also introduce a novel metric, the HOP distance, which is the minimum number of HOPs to transform a tree into another tree. The HOP distance can be computed in near-linear time, a rare instance of tree rearrangement distance that is intractable. We also describe how the proposed tree representation can be further generalized to tree-child networks, showcasing its versatility and potential applications in broader evolutionary analyses.

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