In article <1993Aug30.200054.13037 at nrcnet0.nrc.ca>,
Paul Berti <Paul.Berti at BRI.NRC.CA> wrote:
>>Does anyone have experience with, or opinions about, calculating
>distances between distantly related sequences?
>>>Anyone care to venture an opinion?
>Biotechnology Research Institute
>National Research Council of Canada
>>Paul.Berti at BRI.NRC.CA
We have developed the math and the programs to compute the
variance of the PAM distance between two sequences. That is,
assuming a markovian model of evolution, then after a given
amount of evolution, the measured PAM distance is a random
variable. We can estimate the variance of this distance,
and hence conclude confidence intervals of distances, and
more importantly confidence of the assertion "X is farther
appart from Y than Z".
All of this is available in Darwin, which is our system for
doing sequence analysis.
best wishes, Gaston Gonnet, ETH, Zurich.