Figure 1

DNAAlignEditor view of an example alignment. The color coded cells represent the base calls and the numbers within the cells reflect the quality scores. Insertion/deletions are present in columns 576–578 and 591, and SNPs in columns 579, 580, 594, 597, 599 and 603. Below the alignment are the buttons used to manipulate sequence. To the left of the alignment are the names of the individuals displayed. Above the alignment are identification summary statistics on the alignment and additional buttons to manipulate sequence file and re-CLUSTAL functions.