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Add a global list of best trees that will be updated from the per-round list at the end of each round.

Allow using custom characters in sequence alignments and their interpretation. As Lars put it:

"Define the set of characters deemed certainties (e.g., “-d A,C,G,T”, which would imply a 4 x 4 matrix, “-d A,C,G,T,R,Y”, which would imply a 6 x 6 matrix (could be relevant for SNP data), “-d A,C,G,T,R,Y,K,M,S,W”, which would imply a 10 x 10 matrix (could be relevant for SNP data). If we were to want to analyse di-nucleotide data, we would define the certainties as “-d AA,AC,AG,AT, …, GT,TT”, and if we wanted to analyse codons, the same approach would be used. Because users define characters that are deemed certain, the (1) size of the matrix (Markov model) will be known and (2) the other characters in the data will be considered uncertainties."