I would like to compare two bacterial genomes using tblastx for subsequent visualization in ACT (artemis).
Here is my tblastx command:
tblastx -db reference_genome -query query_genome.fas -out comparison.txt -outfmt 7 -num_threads 8 -evalue 1e-5
I got only 400 hits and all of them have evalues of 0.0 (blastn for example give me almost 8000 hits, and the evalue is variable).
I believe that something is filtering the results, but it is not clear to me.