DAWGPAWS is a suite of command line programs written in Perl that accelerates annotation of genes and transposable elements in plant genomes by automating the process of running annotation programs and facilitating combined evidence annotation curation.
- Conversion of ab initio gene and TE annotation from native format to GFF2 and GFF3 format
- Ab initio gene annotation in high throughput batch mode
- Ab initio transposable element annotation in high throughput batch mode
- Command line interface
I wrote it, and recommend it.