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DNA vs amino acid sequences

Mark Siddall mes at zoo.toronto.edu
Fri Jun 16 00:05:36 EST 1995

In article <3rghpv$hm6 at nuscc.nus.sg> mcbbv at leonis.nus.sg (Venkatesh Byrappa) writes:
>Dear netters,
> I am now in the process of generating a phylogenetic tree of actin
>sequences from some lower
>vertebrates.  I am wondering which sequence I should use - DNA or amino
>acid? Which is more appropriate for a highly conserved protein like the

Your question is a wise one, yet it cannot be answered except empirically.
It may be that it is so conserved in the scope of your question that 
aa does nto resolve all groups.  It may be so poorly conserved that 
bases lead to inordinate homoplasy.
I would recommend taking an "experimental" approach to the issue.  That is
look to see how sensitive your groupings are to different ways of 
handling the data.
1) aa translation only.
2) all bases equal weight
3) first and second position only
4) first and second position weighted heavier than third but still count third
5) all sites subject to TS/TV weighting.
6) first and second weighted to the same weight as TV in third and TS in
   third weighted less.

Don't forget to consider the possibility of counting gaps.


> Can someone lead me to recent publications that compare the
>pros and cons
>of using DNA vis-a-vis amino acid sequences for generating phylogenetic

Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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