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Currently the smallest span of score values in the substitution matrix or profile must be 1. (Will be fixed shortly)

Ariadne will only find the optimal alignment between each pair of sequences - ie it does a single-pass Smith-Waterman comparison. Prospero will find all suboptimal alignments. Ariadne will be modified in the next release to find all significant subalignments. Fixed in V1.3

The formula for statistical significance has been thoroughly tested on standard substition matrices (ie the PAM and BLOSUM series). If you use it on other matrices/profiles and get unexpected results please contact me.