Merge two overlapping nucleic acid sequences
emboss
merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto
You can view the original documentation here_.
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html