title: A brief review of software tools for pangenomics.
abstract: Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: xiaojf@big.ac.cn.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Zhewen
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jiayan
authors.initials: J
authors.lastname: Wu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology; D016208:Databases, Factual; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012984:Software
keywords: Comparative analysis; Core genes; Genomic dynamics; Pangenome; Pangenomics