Deprecated. All classes within the kea.phylogeny.dissimilarity package have been superseded by those in the kea.phylogeny.distance package. All distance values calculated here assume a gap penalty of 1. This is not necessarily incorrect, but is not consistent with distance values calculated by Phylip and Treecon, for example. To replicate output from these programs use classes within the kea.phylogeny.distance package, with a gap penalty of 0.