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arXiv · 2511.17996

CLTree: A Tool for Annotating, Rooting, and Evaluating Phylogenetic Trees Leveraging Genomic Lineages

Guanghong Zuo
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Abstract

Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a rooted tree. For an unrooted tree, it determines the root that best conforms to the taxonomic system based on the aforementioned lineage annotations. Based on the lineage annotations of notes, CLTree infers the monophyly of taxonomic units and quantifies the concordance between the phylogenetic tree and the taxonomic system base on Shannon entropy. The core algorithm of CLTree is highly efficient with linear complexity, capable of processing phylogenetic trees with 17,955 terminal nodes within one second. We believe that CLTree will serve as a powerful tool for study of evolution and taxonomy.

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Guanghong Zuo. 2025-11-22. CLTree: A Tool for Annotating, Rooting, and Evaluating Phylogenetic Trees Leveraging Genomic Lineages. https://arxiv.org/abs/2511.17996

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