Why doesn't ClustalW2 (running under Linux for teaching purposes) behave correctly when we choose scoring matrices other than Gonnet's?

16 March 2015 1 8K Report

When we choose the BLOSUM series of matrices for the initial pairwise alignment step, all the pairwise alignments score 0. The subsequent progressive alignment phase does not work correctly either. In the resulting alignment, each sequence is aligned against gaps in all the remaining sequences. Has anybody else experienced this problem? Any idea on how to fix it?

Héctor Candela

I just realized the problem occurs only when we run the program using the menus. When the parameters are specified in the command line, everything seems to be fine.

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