Choosing an algorithm

Hello,
this could be a silly question. According to the documentation, one can choose between three algorithms: Dekker, Needleman-Wunsch and MEDITE. I do not know how to specify that in the python collate function. Any idea?

[djbpitt]

@moh55m55 @rhdekker Not a silly question at all. The Java version of CollateX lets the user select different collation methods. The Python version supports a single method, so there is no need to specify.

Thanks. What is the method the python version supports?
I see two methods: EditGraphAligner and ExperimentalAstarAligner

[djbpitt]

@moh55m55 @rhdekker The default in the CollateX Python port is EditGraphAligner. You can use ExperimentalAstarAligner by specifying astar=True as a parameter to the collate() function. I haven’t tested the Astar aligner and I don’t know how “experimental” it is, that is, whether it is sufficiently functional to produce useful output.

Thanks. Is the EditGraphAligner based on the Needleman algorithm?

[rhdekker]

@moh55m55 @djbpitt Yes, but with enhancements to lower the cost of the token matching and to align more than two witnesses.

Thanks,
What is the alignment score used in EditGraphAligner? the scoring schemes (match, mismatch, and gap)?