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,

http://www.santafe.edu/

 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,

Luc




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

> Dear molbio.evolution readers,
>=20
> 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=
ny
> papers or references where people attempted similar projects?
>=20
> If I do go ahead with this project, I need to establish a reasonable ra=
nge
> 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=
re
> I could find the average size and cause of insertion and deletion
> mutations would be helpful.=20
>=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:
<http://evolution.genetics.washington.edu/phylip/software.html>

--=20
Niklas Wikstr=F6m
Dept. of Botany
Stockholm university
S-10691 Stockholm
SWEDEN
e.mail: wikstrom at botan.su.se

--=20
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
At Home : Tel. 32 (0)15 315886; Fax 32 (0)15 320598



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