Hi I uploaded the MUmmer, did the make check and then make install and everything is correct. But I was using another program (Mix) and when I put the command: serv@Serv:~/MIX-master$/preprocessing.py nucmer --maxmatch -c 30 -l 30 -banded -prefix=alignments /home/serv/MIX-master/contigs.fa Usage: preprocessing.py [options] preprocessing.py: error: no such option: --maxmatch I got problems. Soon I took the Nucmer again and put the command to test if it was working, command: sudo apt-get install nucmer...