In my opinion, it does not matter which gene you shall
use. As long as you shall keep in mind that the resulting
phylogeny tells you about the gene and not necessarily the
organism you study. I know little about RNA-editing in
the organisms you study. However, if similar to plant
mt-genes this mechanism is also at work, you should avoid
including genes affected by it. Unless of course you are
willing to obtain and analyse corresponding cDNA sequences.
Hoping that this was of some help,
Best wishes,
Alfred E. Szmidt
In article <CwA81s.31y at zoo.toronto.edu>, mes at zoo.toronto.edu says...
>>>I'm about to start on a project investigating the molecular phylogeny
>of 2 different groups. One is leeches, the other is a wierd group
>of protists.
