The function DrawSimPam produces a graph of the similarity score against different PAM distances for a given alignment. This gives the user an intuitive notion of how the similarity changes with changing distances, how precisely defined the maximum is, etc. For example:
> DB := ReadDb('~cbrg/DB/SwissProt'): CreateDayMatrices(): > m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))): > m := LocalAlignBestPam( m, DMS ): > DrawSimPam(m); The maximum, 275.4, is located at pam=84The results are contained in Figure .
Like all Darwin functions producing graphic files, the results of a DrawSimPam are stored by default in the file temp.ps in the current directory. Chapter - Randomization, Statistics and Visualization contain a complete description of options and protocols for graphic output.