Find differences between nearly identical sequences emboss diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto Sequence 1 Sequence 2 Wordsize Report differences at the ends No Yes Output Report File Format Diffseq EMBL GENBANK GFF PIR SwissProt DbMotif Excel (tab delimited) FeatTable Motif Regions SeqTable SRS Simple SRS Table TagSeq Sequence 1 Output Feature File Format GFF EMBL SwissProt Sequence 2 Output Feature File Format GFF EMBL SwissProt You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html