INSTRAL: discordance-aware phylogenetic placement using quartet scores

Phylogenomic analyses have increasingly adopted species tree reconstruction using methods that account for gene tree discordance using pipelines that require both human effort and computational resources. As the number of available genomes continues to increase, a new problem is facing researchers. Once more species become available, they have to repeat the whole process from the beginning because updating species trees is currently not possible. However, the de novo inference can be prohibitively costly in human effort or machine time. In this paper, we introduce INSTRAL, a method that extends ASTRAL to enable phylogenetic placement. INSTRAL is designed to place a new species on an existing species tree after sequences from the new species have already been added to gene trees; thus, INSTRAL is complementary to existing placement methods that update gene trees.系统发育基因组学分析（phylogenomic analysis）愈发普遍地采用可处理基因树冲突（gene tree discordance）的方法开展物种树重建（species tree reconstruction），这类方法所依托的分析流程既需要人力投入，也需消耗大量计算资源。随着可用基因组数据量的持续增长，研究者正面临一项新的挑战：一旦新增可获取的物种数据，研究者就必须从头重复整个分析流程，因为当前尚无可行的物种树更新方案。然而，从头推断（de novo inference）所需的人力与机时成本往往高得难以承受。本研究提出INSTRAL——一种对ASTRAL进行扩展以实现系统发育放置（phylogenetic placement）的方法。INSTRAL的设计目标是，在新物种的序列已被加入各基因树后，将该新物种放置到已有的物种树之上；因此，INSTRAL与现有的更新基因树的放置方法形成互补。