[Taxacom] base alignment
Jan De Laet
jan.de.laet at skynet.be
Tue Aug 29 13:21:39 CDT 2006
pierre deleporte wrote:
>A 12:28 29/08/2006 -0400, John Grehan wrote:
>>I am just giving my impression of what I have
>>read so far. For example, one paper I read stated that alignment uses
>>distance measures which to my understanding is not cladistic.
>Alignment can effectively be done on the basis of overall similarity.
There seems to be some slippage of meaning going on here. Using distance
measures does not necessarily amount to using overall similarity. It all
depends on which diatance is being used. In cladistic analysis, the
length of a tree can be framed in terms of Manhattan distances, and a
most parsionious tree is a tree on which that distance is minimal. Does
that make cladistics a method that maximizes overall similarity? Not if
you ask me.
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