Differences with ClustalW2

The current implementation provides different results from the original ClutalW mainly for identity score and some features not described in original papers:

• Identity score: it was not possible to replicate the distance score of original ClustalW. The scoring function is for sure "1 minus the number of identities in the best alignment divided by the length of shorter sequence" (checked in the original ClustalW code). What is different is the result of the pairwise alignment, some domains seem to be cut, probably is a local alignment with gotoh feature. This is an essential point for MSA, therefore it is impossible to obtain the same result.

• Many important variables are scaled in original code (like gap, weights, etc.), also the normalization of the weights of guide tree is different from that one described in reference paper.

• Weight matrices: In original papers the distances are measured directly from guide tree to select the right substitution matrix, in current implementation the matrix is selected by average percent indentity of sequences. This feature is imported.

• Initial gap penalties: depending on the substitution matrix choosed a scaling factor is applied (e.g. 0.5 for Blosum30). This feature is imported.