Following on from AHRD functional annotation program (error), the functional annotation program AHRD (https://github.com/groupschoof/AHRD) appears to require the results from blastp searches of proteins to various databases (sprot, trembl etc.) to be in blastall pairwise format instead of blast+ pairwise format.
Does it make a difference whether I use blastall or blast+? It seems the use of blast+ is recommended by NCBI - would the results be better using blast+?
Is there a script already available which can convert blast+ pairwise format files to blastall pairwise format files? (I have lots of blast+ generated files which I would like to use if possible).