PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Michael R. McKain et al.   BIOINFORMATICS

Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology

(2015) Ralph Bock   Annual Review of Plant Biology

Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology

(2015) Marcelo Rogalski et al.   Frontiers in Plant Science

Plann: A Command-Line Application for Annotating Plastome Sequences

(2015) Daisie I. Huang et al.   Applications in Plant Sciences

Plastid phylogenomics and green plant phylogeny: almost full circle but not quite there

(2014) Charles C Davis et al.   BMC BIOLOGY

The potential of genomics in plant systematics

(2013) Douglas E. Soltis et al.   TAXON

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

(2012) Chang Liu et al.   BMC GENOMICS

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS