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