In article <94227.143105SVM1 at psuvm.psu.edu>,
Spencer Muse <SVM1 at psuvm.psu.edu> wrote:
>At the risk of adding to the confusion here, I bring up a point that has
>troubled me for a while now. There seem to be two versions of "transition/
>transversion ratio"floating around. Some folks use, say, the Kimura 2 parameter
>model to estimate S, the expected number of transition changes, and V, the
>expectd number of transversion changes, and then use the ratio of these two
>estimates to estimate R=S/V. On the other hand, others will use the same model,
>which has in its rate matrix parameters s (for transitions) an v (for
>transversions), and estimate the parameter r=s/v. It seems to me that the
>latter route is more appropriate.
...
>I don't know which parameter we are allowed to control in
>Phylip (I hope Joe will tell us),
It's the latter, if I understand you correctly. The ratio of the total
expected instantaneous rate of transitions over the same thing for
transversions. Definitely _not_ the ratio of the number of net transition
differences to the number of net transversion differences. I agree that the
ratio of instantaneous rates is the most natural definitions.
> but I'm not sure why it should be
>necessary to perform multiple runs. If a 2 parameter model, such as Kimura or
>its extension by Hasegawa et al. (1985) is used, the information falls out
>immediately. It also does not force the same ts/tv ratio on all branches of
>the tree (whether that is a plus or minus, I'm not sure). Of course, it does
>require estimation of 2 parameters per branch rather than one, but the
>computing expense there is minimal, especially when considered next to the cost
>of searching through tree space.
If you restrict all branches to have the same ratio of transitions to
transversions, then it is not so simple a matter to calculate the optimal
ratio for a single tree, so we need some more effort. My current programs do
not do any optimizing of this parameter, for reasons of computational
difficulty.
Allowing the ratio of transitions and transversions to vary arbitrarily
widely between branches of the tree strikes me as an overreaction, (of course,
so is our current practice of allowing no variation).
-----
Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
Internet: joe at genetics.washington.edu (IP No. 128.95.12.41)