Modeling molecular evolution

Luc De Bry luc.de.bry at POPHOST.EUNET.BE
Mon Jan 20 05:31:05 EST 1997

In addition, you may also enjoy to surf to the Santa Fe Institute,


 to learn about the work of Prof. Stuart Kaufman.

In his 1993 book,
The Origins of Order
Self-Organization and Selection in Evolution
Oxford University Press
ISBN 0-19-507951-5 (pbk),

he is covering a substantial part of the answer to Airlie's question.

Enjoy it, with kind regards,


In article <airlie-1101971855340001 at ip157.harvey.la.pub-ip.psi.net>,
airlie at mindspring.com (Airlie Sattler) wrote:

> Dear molbio.evolution readers,
> I am thinking about writing a program to model sequence evolution.
> Basically I want to be able to (1) input a known sequence (2)mutate it
> using a range of mutation rates and types(ie base pair changes,
> insertions, deletions) (3) use my artificially created sequences as a
> control group for alignment and phylogenetic analysis. Do you know if
> someone has written a program which does this already? Do you know of a=
> papers or references where people attempted similar projects?
> If I do go ahead with this project, I need to establish a reasonable ra=
> of mutation rates / sequence generation (How to set my molecular clock).
> If you know of any source for background mutation rates in different
> organisms, that would be a great resource. Also any basic reference whe=
> I could find the average size and cause of insertion and deletion
> mutations would be helpful.=20
> Thank you for any feedback you might have about this project.

John Hulsenbeck has written a program called TheSiminator and Andrew
Rambaut and Nick Grassly has written Seq-Gen (Sequence Generator). Both
programs could be something you want. You can check out the information
about them at the phylogeny program page maintained by Joe Felsenstein.
The page is:

Niklas Wikstr=F6m
Dept. of Botany
Stockholm university
S-10691 Stockholm
e.mail: wikstrom at botan.su.se

Luc De Bry, Ph.D.; Head of Research Department; DANONE BISCUITS NORTH
De Beukelaer-Pareinlaan 1; B-2200  Herentals  -  Belgium
Tel. 32 (0)14 241432; Fax 32 (0)14 241025; Email :=20
luc.de.bry at pophost.eunet.be
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