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transition/transversion calc?

Kent Holsinger kent at DARWIN.EEB.UCONN.EDU
Mon Aug 15 16:05:37 EST 1994

>>>>> "Steve" == <HARDIES at thorin.uthscsa.edu> writes:

    Steve> Joe Felsenstein writes (in response to a question by Tom
    Steve> Doak):
    >> By doing multiple runs with DNAML from PHYLIP, at each at a
    >> different value of the transition/transversion ratio, and
    >> picking the result that achieves the highest likelihood, and
    >> also saving that tree, one will get a joint ML estimate of the
    >> ratio and the tree.  I think that is what you want.

    Steve> Do you think it would be useful (when using the above
    Steve> method) to obtain the transition/transversion ratio from a
    Steve> subset of the most closely related sequences to suppress
    Steve> noise caused by saturation of transitions at greater
    Steve> divergence?

Joe can answer this more authoritatively than I, but in principle
there should be no need to restrict the method to a subset of the most
closely related sequences.  DNAML includes a model of the
substitutional process that will correct for multiple substitutions.

In practice, the model has to assume the *same*
transition/transversion bias applies across the entire tree.  Whether
that's a reasonable assumption will depend on the particular data set.
If you have enough data it would be possible, I think, to estimate the
ratio separately in two or more different sets of taxa and use a
likelihood ratio test to determine whether they are different.  DNAML
also assumes that all sequence difference are a result of nucleotide
substitution, not indels.  Thus, it should be used only on portions of
seqeuences where the alignment is good.

-- Kent

| Kent E. Holsinger                 Internet: Kent at Darwin.EEB.UConn.Edu  |
| Department of Ecology &                     Holsinge at UConnVM.UConn.Edu |
|    Evolutionary Biology           BITNET:   Holsinge at UConnVM           |
| University of Connecticut, U-43                                        |
| Storrs, CT   06269-3043                                                |

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