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package have been superseded by those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.