Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes

MOTIVATION: Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects. RESULTS: Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware. AVAILABILITY AND IMPLEMENTATION: Verdant is available at: http://verdant.iplantcollaborative.org/plastidDB/. It is implemented in PHP, Perl, MySQL, Javascript, HTML and CSS with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.