Hey guys,

I run exonerate with the following settings: exonerate -t file1.fasta -q file2.fasta --model protein2genome --bestn 1 --ryo ">%qi %qd\n%qas\n" --showquerygff yes --maxintron 30000 --showtargetgff yes--percent 70

It generated a c4 alignment as well as querry/target sequences and some information on gff, all together within a file.

Do you know how I can get only gff files? My goal is to use the gff file to extract aligned sequences (fasta format) from querry/target input files.