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 ...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.展开更多
基金supported by the National Key R&D Program of China(2018YFA0903200)Science Technology and Innovation Commission of Shenzhen Municipality of China(ZDSYS 20200811142605017)It was also supported by Innovation Program of Chinese Academy of Agricultural Sciences and the Elite Young Scientists Program of CAAS.
文摘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.
