Clustering of Positions in Nucleotide Sequences by Trim Distance

A trim distance is a measure for comparing positions in nucleotide sequences based on phylogenetic trees. In this paper, first we formulate another trim distance based on the MAST distance, in contrast to the previous trim distance based on the LCA-preserving distance. Next, we apply a group average method in agglomerative hierarchical clustering to the positions in nucleotide sequences by the trim distances to nucleotide sequences of influenza A (H1N1) viruses at 2008 as non-pandemic viruses and at 2009 as pandemic viruses, with introducing the following two methods of clustering. The clustering of separated positions is one method of clustering whose positions in nucleotide sequences at 2008 are separated from those at 2009. The clustering of mixed positions is another method of clustering whose positions in nucleotide sequences at 2008 are mixed with those at 2009.