Modeling molecular evolution

Niklas Wikström wikstrom at botan.su.se
Mon Jan 13 10:10:44 EST 1997

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 any
> papers or references where people attempted similar projects?
> If I do go ahead with this project, I need to establish a reasonable range
> 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 where
> I could find the average size and cause of insertion and deletion
> mutations would be helpful. 
> 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 Wikström
Dept. of Botany
Stockholm university
S-10691 Stockholm
e.mail: wikstrom at botan.su.se

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