How accurate are PAM distances?

Gaston Gonnet gonnet at inf.ethz.ch
Wed Sep 1 11:38:20 EST 1993

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?
>Paul Berti
>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.

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