[Taxacom] base alignment

[Jan De Laet]

Hi all,

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.

Best

   -- Jan
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