How To Translate Old Parameters In New Version Of Blast 2.2.27 +

Question

[konstantinkul]

Hi, I am a beginner in blast. I can't figure out how to write options for the new version of blasts. I read manuals, but it confused me more.

How to translate this options for new version of blast

-F "m S"
-F "m D"
-F "m C"

and

-f  for blastx

I would be grateful for any advice.

Answer 1

[Lee Katz]

Blast+ comes with a legacy_blast.pl script that you can use. If you do a command such as legacy_blast.pl blastall ... then all your parameters will be equivalent. This should be exactly an answer to your problem.

[konstantinkul]

Thanks, Lee! You saved me again!

[Lee Katz]

I'm glad I helped you out!