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During development were highlighted and fixed two bugs in the Align2 package:
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buildscore method in Sustitution.cc: The calculation is incorrect if is used a matrix with character '-' (e.g. blosum62.dat). Character '-' has ascii value 45 which added to 32 is 77 that is 'M' (and vice versa). Consequently scoring loaded for the Methionine is incorrect.
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gap penalities position in NWAlign.cc was wrong
The current implementation of the Needleman-Wunsch does not properly supports gap penalities leading to suboptimal alignments, bad for progressive alignments and initial distance matrix. To obtain correct optimal alignment has been implemented the algorithm Needleman-Wunsch-Gotoh global alignment. Now the result of pairwise alignments obtained score is identical to those of Emboss needle (with end gaps on).
The algorithm can be used with
subali --in samples/pair.fasta --gotoh -o 10 -e 0.5
In the example the score improves from 440 to 448.5. The suboptiomal alingments have not been implemented.