title: Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  mrmckain@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: McKain
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Ryan H
authors.initials: RH
authors.lastname: Hartsock
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Molly M
authors.initials: MM
authors.lastname: Wohl
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kellogg
mesh_terms: D030561:Databases, Nucleic Acid; D054628:Genome, Chloroplast; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software