I am writing a function which takes aligned sequences, and outputs a consensus sequence using IUPAC ambiguous nucleotides. I am unsure how to handle assignment at a given position if gaps are the mode character. Here is an example.
Sequence 0 G-ATGT
Sequence 1 G-ATGT
Sequence 2 G-ATGT
Sequence 3 GCATGT
What would the appropriate consensus sequence in this case be?