Script that resolves ambiguous nucleotides in sequences from alignment in fasta-format using the rest sequences in dataset:

• discards sequences with too many ambiguous characters (e.g. 0.2%), which may be a sign of poor sequence quality rather than natural heterogeneity;
• in the remaining sequences, identifies a region (e.g. 100 nt) with an ambiguous character and blasts it against the dataset;
• identifies the frequency of different nucleotides at this position in the most closely related sequences;
• replaces the ambiguous character with the most common nucleotide among the most closely related sequences.