CPStools: A package for analyzing chloroplast genome sequences

Abstract

CPStools is a user-friendly software for comprehensive chloroplast genome analysis. It integrates 10 functionalities including Genbank file checking, statistical information generation, sequence adjustment, inverted repeat (IR) regions identification, nucleotide diversity (Pi) analysis, relative synonymous codon usage (RSCU) calculation, simple sequence repeats (SSRs) identification, long sequence repeats (LSRs) statistics, phylogenetic analysis, and format conversion. CPStools handles Genbank or Fasta format inputs, delivering results comparable to other tools while excelling in data preparation for advanced analysis. It uniquely generates consensus merged protein-coding sequence (CDS) or protein sequences from multiple Genbank files, facilitating advanced phylogenetic analysis. CPStools offer reliable results for comprehensive chloroplast genome analysis.