ORPA: A Fast and Efficient Method for Constructing Genome-Wide Alignments of Organelle Genomes for Phylogenetic Analysis

SUMMARY 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 have developed a speedy and efficient method called ORPA. ORPA quickly generates multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST, completing the task in just one minute. With increasing data volume, ORPA’s efficiency is even more pronounced, over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes. The tool’s phylogenetic tree outputs demonstrate equivalent results 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.