v0.3.1

Fixes

• Optional arguments were not obeyed anymore due to the new minimization process.
• Kmer based distances are now computed by taking into account common Kmers and common missing Kmers, in conformity with the Simple Matching Distance (by opposition with the Tanimoto Distance used previously). Kmers based distances seem to not be suitable when comparing unrelated sequences of various length. By taking into account also the Kmers that are commonly absent, these sequences are relatively disfavoured instead of appearing more related due to their size.