[Taxacom] DNA homologies

[Richard Zander]

Alignment is a problem in part because it is usually presented as an
optimal alignment, and suboptimal alignments may cause a change in a
branch arrangement of interest. New software helps deal with the joint
probability:
http://www.biomath.medsch.ucla.edu/msuchard/bali-phy/
and possibly POY does the same.

Now we need a joint probability estimate for support for a branch
arrangement that takes into account any uncertainty contributed by a
different, suboptimal outgroup. One way is to use multiple outgroups,
and, then check the second outgroup to see if it changes the branch
arrangement if it is used as the only outgroup, and if it does, then
multiply the support value for the branch arrangement by the support
value for the optimal outgroup as sister to the tree being analyzed.

Comments? Using alignment and outgroup optima are the two most
problematic assumptions, I think, that affect molecular evolutionary
analysis.

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Richard H. Zander 
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