This data visualization module provides a graphical view of the nucleotide character variation in a barcode data set. It allows the user to quickly pinpoint nucleotide positions within the barcode sequence that account for barcode variation in a set of species. The tool takes a FASTA alignment of barcode sequences (or the alignment of unique haplotypes created in the Haplotype Analysis tool from a given barcode dataset) as input and and highlights variable positions across the barcode sequence in an easy-to-read format. It also shows the nucleotide position for each variable site (counting from 5' to 3') as well as the codon position they belong to. It is therefore important that the FASTA file of the barcode sequences is in the correct reading frame.
The HapMap tool works best for focused character-based analysis of a limited number of taxa (i.e. in a species complex or when dealing with cryptic species) as a complement to distance-based methods such as Neighbour-joining analysis.