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

Table 1 Comparison of existing plastome annotation tools

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

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

ISSN: 1746-4811