I've recently run two searches, one with blastall (from legacy blast) and one with modern blastn. Both versions are 2.2.25 (the most recent).
The blastall search is: blastall -i test.fasta -p blastn -d old_formatted_database -m 8 -e 1e-10
The blastn search is: blastn -query test.fasta -db new_formated_database -outfmt 6 -evalue 1e-10
Note that the two databases have each been created with the program's respective formatdb utility.
The blastn search yields 3 results, while the blastall search results in over 50. Why is this? I realize the programs themselves are not readily comparable, but I was under the impression that their output should be similar since they're based on the same scoring methods.
From a more theoretical point of view, shouldn't there be an exact number of hits matching a given query sequence and scoring scheme? Shouldn't these all be reported regardless of the blast approach used?