Similar to the scripts align.*, this program is an example to show how to align two sequences. This program is very primitive and meant only as an example:

• there is little error handling
• it takes two files containing sequences (no fasta format, only the sequence)
• the parameters to the aligner are hard coded

Make sure that you installed mummer library properly. The following command should print "OK": pkg-config --exists mummer && echo OK. If not, check the followings:

• that you ran make install
• if you used --prefix /path with ./configure, you may have to append /path/lib/pkgconfig to the environment variable PKG_CONFIG_PATH.

Now make should create the executable align.