Choosing an algorithm

[ghost]

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.

[ghost]

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.

[ghost]

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.

[ghost]

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