All of the above mentioned alignment methods are fully automated, i.e., they construct alignments following a fixed set of algorithmical rules. Most methods use a well-defined objective function assigning numerical quality score to every possible output alignment of an input sequence set and try to find an optimal or near-optimal alignment according to this objective function. In this process, a number of program parameters such as gap penalties can be adjusted. While the overall influence of these parameters is quite obvious, there is usually no direct way of influencing the outcome of an alignment program.