Invariable sites question

Korbinian Strimmer strimmer at zi.biologie.uni-muenchen.de
Tue Nov 26 12:12:15 EST 1996

On 25 Nov 1996, James McInerney wrote:

>  With the latest
> version of PAUP you can 'remove' (mathematically, not physically) a
> proportion of invariable sites (which must be calculated by ML), for ALL
> pairwise distance methods.

I haven't seen PAUP* so far (it's not out yet, is it?)  but removing sites
'mathematically' should be simply incorporating f (or whatever other
parameter) in the likelihood function so that all pairwise distances
and all branch lengths on trees can account for invariable sites. 

Whether one is using PAUP* or DNAML or whatever to calculate the ML
distance I think one other question seems to be important:  How
are the base frequencies estimated?  In theory, you have to differentiate
between the base frequencies for the variable positions (= stationary
frequencies of the underlying Markov model) and the bas frequencies
of the invariable sites (= probability to see a given  pattern
- say AAAAAAAA - at an invariable site).  It seems to me that now
simply the avarage frequencies are used over the complete data set
for both sort of frequencies though they have a completely different
meaning (this is done in Hasegawa et al papers, in one of Adachi et al
paper, in some Churchil et al papers ) etc.  SO, what really interests
me, how is this accounted for in PAUP* (I think it is not considered
in DNAML, is it?)


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