Doug.Eernisse at um.cc.umich.edu writes
> Without wanting to start any small or large battles, it seems
>to me that distance methods, especially UPGMA, should be much more
>prone to the general problem of partial representation in the
>sequences. In parsimony, the stretch of sequence lacking for a
>particular sequence does not influence the resulting topology.
Yes, unles the lacking stretch is large. This will cause an artificial
decrease in substitution rate in some branches and hence may lead to
the inconsistency of the parsimony method.