The revised DNA Master Annotation Guide is available on PhagesDB and the sea-wiki.  Below are some important revisions to note.

• The process for submitting genomes for annotation QC has changed slightly.  You are asked to submit two .dnam5 files.  Particular attention to functional calls is needed.
• Start-site decision-making has been modified to use the Karlin/Kaplan scoring matrices (NOT DNA Master SD scores).
• Starterator: A new program is available for evaluating start-site options in the context of similar phages/genes.
• GeneMark’s servers were hacked, so program choices have changed.
• NCBI BLAST parameters have changed, so BLASTing whole genomes requires additional care.

Check out the What’s New document for further explanation!

Thanks for your input!