Mark Siddall writes:
>I agreee with Erich here. If it doesn't do parsimony, it must be
>distance-based. If it's distance based, it's phenetic. If it's
>phenetic it's not phylogenetic.
>It's hard to believe this still has to be said after all of these years!
>>mark
>
A lot of definitions!
The main purpose of tree-construction is to reconstruct a REAL tree.
If distances among OTU are estimated correctly (read: proportionally
to time), the distance-based approach will infer rather correct tree.
It was shown in many examples that the parsimony often gives biased
result even though it is "phylogenetic". If the latter means "incorrect",
why should I prefer it?
It is hard to believe but all these years convinced me that the parsimony
is not better than distance-based methods.
Andrey
