Abstract: The invention provides an automated method of identifying a plurality of different polymorphisms within two or more related nucleic acid sequences. The method consists of: (a) obtaining a data set comprising a nucleic acid sequence assembly and a plurality of sequence characteristic parameters associated with said assembly; (b) indexing said nucleic acid assembly and said plurality of sequence characteristic parameters in a database; (c) selecting a region of said nucleic acid assembly having sequence characteristic parameters indicative of a polymorphic sequence, and (d) displaying two or more nucleic acid sequences of said region, said two or more sequences identifying different polymorphisms within said nucleic acid assembly. Also provided is a method of identifying a nucleic acid containing an indel region within a set of related nucleic acid sequences.