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Table 1 Comparison of existing plastome annotation tools

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

Tools Operating system User interface Time Approach Post-annotation algorithms for identification of feature boundaries Output file format Log file References
DOGMA Windows, Linux, Mac Web 5–10 min Target against reference No table No Wyman et al. [12]
CpGAVAS Windows, Linux, Mac Web ~ 1 h Target against reference No GFF3 and GenBank No Liu et al. [13]
Plan Windows, Linux, Mac Console ~ 30 s Target against reference No tbl Yes Huang and Cronk [16]
Verdant Windows, Linux, Mac Web 10–30 min Target against reference Yes GFF3 No McKain et al. [14]
GeSeq Windows, Linux, Mac Web 6 s–13 min Target against reference No GenBank No Tillich et al. [15]
PGA Windows, Linux, Mac Console ~ 20 s Reference against target Yes GenBank Yes This study
  1. For PGA, a laptop equipped with 2.5 GHz 4-core Intel core i3 processors and 8 GB memory was used. Runtimes for other tools were derived from the corresponding references. The phrase “target against reference” signifies a BLASTN or TBLASTN search of a target plastome against an annotated reference plastome, whereas “reference against target” signifies a BLASTN or TBLASTN search of an annotated reference plastome against a target plastome