ORPA: a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

文献类型： 外文期刊

第一作者： Bi, Guiqi

作者： Bi, Guiqi;Luan, Xinxin;Yan, Jianbin;Luan, Xinxin

作者机构：

关键词： Ultrafast alignment; Organelle phylogenomics; Phylogenomic conflict; Efficient pipeline; Multiple sequence alignment pipeline

期刊名称：JOURNAL OF GENETICS AND GENOMICS （ 影响因子：5.9； 五年影响因子：5.9 ）

ISSN： 1673-8527

年卷期： 2024 年 51 卷 3 期

页码：

收录情况： SCI

摘要： Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually, a process that can be time-consuming and prone to errors. The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations. The processing of a large number of sequences, however, remains a time-consuming task. To conquer this challenge, we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis (ORPA). ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST, completing the task just in 1 min. With increasing data volume, the efficiency of ORPA is even more pronounced, over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes. The phylogenetic tree outputs from ORPA are equivalent to HomBlocks, indicating its outstanding efficiency. Due to its speed and accuracy, ORPA can identify species-level evolutionary conflicts, providing valuable insights into evolutionary cognition. Copyright (c) 2023, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved.

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