The Alignment Scores command (which is available from the gap4 Options menu) may be used to adjust the gap open and gap extension penalties for some of the alignment algorithms used within gap4. At present this will affect all alignments except the Find Internal Joins function and most of the assembly algorithms.
For dealing with sequences where the alignment differences have been caused by real evolutionary events, these parameters will probably need changing from the defaults. The default values are set up with the assumption that any alignment differences are due to base calling errors, and hence the gap extension penalty will be high.
The alignment matrix may also be adjusted, but this is not listed in the
dialogue. To do this take a copy of `$STADENROOT/tables/nuc_matrix',
edit the copy, and set the ALIGNMENT.MATRIX_FILE parameter in your
`.gaprc' file.