[Bioperl-l] Bioperl-run: Testing alignments generated externally

Sendu Bala bix at sendu.me.uk
Thu Oct 26 05:48:37 EDT 2006


Nathan Haigh wrote:
> I'm thinking that it's not wise to test for things like
> overall_percentage_identity etc in alignments that are generated by
> external software like T-Coffee, Clustalw etc. Changes to software
> algorithms/efficiency, bug fixes etc may well alter the quality of the
> alignment produced in different versions and thus affect the value
> returned by such methods. Therefore, I think these methods should only
> be tested from alignments loaded directly from t/data.

Did you discover some specific problem cases?


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