Dear Colleagues,
I received many very useful replies to my query for computer programs to
demonstrate experimental evolution, and in general various evolutionary
topics, for students. Thanks so very much to all those who kindly sent
replies and information.
I list below an overview of the suggestions received and further below
replies in full so that they may be of use for others.
Best regards,
Else Fjerdingstad
OVERVIEW:
- PopG by J. Felsenstein (earlier called Simul8)
(ftp://evolution.gs.washington.edu/pub/popgen/popg.html) Free and
downloadable. Allows manipulating fitness of different genotypes,
population size, mutation rates for two different alleles, number of
populations, migration rate between subpopulations, and then carry out
simulations to give a graphic output on allele frequency changes and
allele fixations.
- Populus by D. Alstad (http://www.cbs.umn.edu/software/populus.html/),
free and downloadable, and allows illustrating a large number of
different evolutionary topics (selection, genetic drift, co-evolution,
heritability, genetic drift etc.)
- Ecobeaker (http://www.simbio.com/) a cellular automaton, not free.
- EvoBeaker (http://www.simbio.com/EvoBeaker.html), Not free -one can
download a free demo if teaching at colleges or in highschools. Has
very detailed manuals.
- Darwinian snails, PopCycle and AlleleA1 by J. Herron (the first later
included in modified version in EvoBeaker) Darwinian snails can de
found at (http://wps.prenhall.com/esm_freeman_evol_3) or (http://fac-
ulty.washington.edu/~herronjc/SoftwareFolder/software.html) ;
PopCycle at http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849183-
,00.html , and AlleleA1 at http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849255-
,00.html PopCycle allows setting mutation rates, survival rates and
migration rates for a test population. AlleleA1 is a single locus,
two allele simulation illustrating how the balance among drift,
selection, and mutation influence the rates of change and the
maintenance of variation.
- XLGene, by C. M Austin & R. Carr. Ask for permission to use it
(chris.austin@cdu.edu.au) & (rodney.carr@deakin.edu.au). The program
is allows simulating genetic drift and tweaking various Hardy-Weinberg
population parameters, while giving a graphical output showing
frequency of alleles.
- WinPop 2.5 , P. Nuin, ( http://www.genedrift.org/winpop.php) - an
upgraded version called ----- PopGene.S^2 will be released (contact
P. Nuin : nuin@terra.com.br
- Evolve, distributed by BioQuest:
(http://bioquest.org/BQLibrary/library/evolve.html ) , one must buy a
site-licence or an individual license to access the programs.
- Evotutor ( http://www.evotutor.org/TutorA.html). Very graphical and
treats a series of topics in different simulations (mutation, genetic
drift, adaptation, gene flow, speciation, phylogenetics, sexual
selection).
- Evolution tutorials from Ridley's Evolution textbook which has website
resources - one of which are virtual experiments (
http://www.blackwellpublishing.com/ridley/experiments/) Also, the site
below has a lot of lessons for various types of evolution related
questions: ( http://www.indiana.edu/%7Eensiweb/home.html)
- Matlab functions to illustrate a series of evolutionary and population
genetic topics (fitness surfaces, frequency dependent selection,
stochastic fertility selection, fitness under epistasis, genetic drift
and many more) by L. Revel, can be found at
http://iguana.wustl.edu/~liam/evol_theory/matlab/ by following the
link to the old page (more details on running these in the full reply
from Revel listed below, towards the very end.
REPLIES IN FULL:
__________
From: "Lauren Chan" <lmc36@cornell.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 1:19 PM
Subject: Re: Other: experimental evolution computer programs
Hi Else,
The program AlleleA1 by Jon Herron might suit your needs.
http://faculty.washington.edu/~herronjc/SoftwareFolder/AlleleA1.html
It is a single locus, two allele simulation with a lot of really nice
features. I find it very easily to use and it does a great job of
illustrating how the balance among drift, selection, mutation, etc
influences matters to rates of change and the maintenance of variation.
Best,
-Lauren
__________________
From: "Joe Felsenstein" <joe@gs.washington.edu>
To: "Else Fjerdingstad" <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 11:56 AM
Subject: Re: Other: experimental evolution computer programs
There are a number of these. Try "Simulate gene frequencies" in Google.
The one from my lab (which isn't found that way) is:
ftp://evolution.gs.washington.edu/pub/popgen/popg.html
(note this is an "ftp:" URL, not an "http:" one).
J.F.
----
Joe Felsenstein joe@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 357730, Seattle, WA 98195-7730 USA
__________________From: "USORHANNUS" <usorhannus@edinboro.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 12:49 PM
Subject: Programs
� Dear Else,
I think what you are looking for is POPULUS - I use it in my evolution
course. You will find it at
http://www.cbs.umn.edu/software/populus.html/
With best regards,
Ulf Sorhannus
Deparment of Biology
Edinboro University of Pennsylvania
Edinboro, PA 16444
USA
__________________
From: Carmen Bessa Gomes
To: Else.Fjerdingstad@snv.jussieu.fr
Sent: Friday, September 08, 2006 12:50 PM
Subject: Re: Other: experimental evolution computer programs
Dear Else,
For my ecology courses, I often use Ecobeaker, a cellular automaton quite
attractive to students (http://www.simbio.com/). Ecobeaker dicobeaksposes
of several "labs" addressing distinct problems. I use it more for
examining ecological questions than evolutionary, but I think you may
find labs addressing evolutionary issues. In addition, it exists also a
software specific for evolutionary biology named EvoBeaker. I hope this
may be of some use to you and that all is well.
Best regards
Carmen
__________________
From: "Miguel de Navascu�s" <m.navascues@gmail.com>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 10:41 AM
Subject: Re: Other: experimental evolution computer programs
� Dear Else,
There use to be a DOS program called Simul8 or something similar but I do
not know its availability at the moment.
Good luck,
Miguel
Miguel de Navascu�s, BScHon, PhD
http://m.navascues.googlepages.com/
__________________
From: "Miguel �ngel Toro Ib��ez" <toro@inia.es>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 8:51 AM
Subject: RE: Other: experimental evolution computer programs
� I think that the computer program called POPULUS of D. Alstad (University of
Minnesota) is quite useful. It allows not only to play with selection,
genetic drift, etc but also ecological models
Miguel Angel Toro Iba�ez
Departamento de Mejora Gen�tica Animal
Instituto Nacional de Investigaci�n y Tecnolog�a Agraria y Agroalimentaria
(INIA) Carretera La Coru�a km. 7 28040 Madrid ESPA�A
Telf: 34 913476807
Fax: 34 913572293
e-mail: toro@inia.es
__________________
From: "Alexander s. Dixson" <italk2thetrees@yahoo.com>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 8:57 AM
Subject: Re: Other: experimental evolution computer programs
� Hello,
I'm a PhD student studying evolution, sexual selection
and development in an insect system at Victoria Uni,
Wellington, New Zealand. I get various jobs as a
teacher assistant in which evolution simulation
programmes are used.
So far the programs used here are mostly from John
Herron, they are all free to download and may well
meet the requirements you listed in your evoldir
posting.
The link to his site is:
http://faculty.washington.edu/~herronjc/SoftwareFolder/software.html
I have also been working with an instructor here
trying to get the program EvoBeaker taken on for
future courses. It is mentioned on Dr. Herron's site
and is very much more detailed program, a bit more
visually appealing, and much nicer to work with.
A link to this is:
http://www.simbio.com/fr_index.html?/EvoBeaker.html
However, Evolbeaker is not free and requires, I think,
that number of students using be registered to meet
copyright requirement for reprinting the very detailed
manuals for each of the labs on the program. The
company will send instructors a copy of evobeaker for
nothing plus samples of the lab manual paperwork. It's
really good though, I've enjoyed playing around with
it!
Hope this helps.
Kind regards,
Alexander Dixson
dixsonalex@student.vuw.ac.nz
From: "Jean-Nicolas Jasmin" <jjasm035@uottawa.ca>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 8:19 AM
Subject: Re: Other: experimental evolution computer programs
� Ch�re Dr. Fjerdingstaf,
j'ai utilis� le logiciel PopG du Dr. Felsenstein de l'Universit� de
Washington lors d'un cours de g�n�tique � l'Universit� d'Ottawa. Ce
logiciel et ses conditions d'utilisation sont disponibles � l'adresse
suivante:
ftp://evolution.gs.washington.edu/pub/popgen/popg.html
Je crois que le logiciel permet de manipuler toutes les variables que vous
mentionnez dans votre courriel, � l'exception de ceux qui concernent la
structure spatiale des populations.
Au plaisir,
Jean-Nicolas
University of California at San Diego
__________________
From: Mark Schultz
To: Else.Fjerdingstad@snv.jussieu.fr
Sent: Friday, September 08, 2006 8:06 AM
Subject: YES! XLGene. RE: Other: experimental evolution computer programs
Yes, I know a great program. It is called XLGene, and was written by
my supervisor and genetecist Prof Chris M Austin and his biometrician
colleague Rodney Carr. You can contact Chris to ask permission on
chris.austin@cdu.edu.au, or Rodney on rodney.carr@deakin.edu.au I'm sure
they would both be happy for you to use it. The program is perfect for
simulating genetic drift and tweaking various Hardy-Weinberg population
parameters, while giving a graphical output showing frequency of alleles.
Regards, Mark
Mark Schultz
Charles Darwin University
C/- Arafura Timor Research Facility
PO Box 41775
Casuarina NT 0811
Ph: +61 (0)8 8920 9292
Fax: +61 (0)8 8920 9222
__________________
From: "Paulo Nuin" <nuin@terra.com.br>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 1:28 PM
Subject: Re: Other: experimental evolution computer programs
� Dear Else
Take a look on the package WinPop 2.5 at
http://www.genedrift.org/winpop.php
it might not be exactly what you want but it has some good features.
Also we will be releasing an upgraded version of it called PopGene.S^2
soon. IF you have any suggestion for a possible module that can be added
to the program we might try to include it.
Regards
Paulo Nuin
From: "David W. Hall" <davehall@uga.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 12:50 PM
Subject: Re: Other: experimental evolution computer programs
�
Else,
You might try www.evotutor.org.
Cheers,
Dave
From: "JOHANNE BRUNET" <jbrunet@wisc.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 2:45 PM
Subject: Re: Other: experimental evolution computer programs
�
Try Populus. It has both a section on ecology
and one on population genetics. There is also
a book you can buy describing the programs. Easy
to use.
From: Ken Weiss
To: Else.Fjerdingstad@snv.jussieu.fr
Sent: Friday, September 08, 2006 3:18 PM
Subject: Re: Other: experimental evolution computer programs
You might give a look at Populus, free and downloadable.
From: "David H. A. Fitch" <david.fitch@nyu.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 3:29 PM
Subject: experimental evolution computer programs
Hi Else,
For my evolution course, I use the free PopG by Joe Felsenstein:
ftp://evolution.gs.washington.edu/pub/popgen/popg.html
or Evolve, distributed by BioQuest:
http://bioquest.org/
Have fun!
Dave Fitch
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - -
~ David H. A. Fitch ~ \ / / /
~ Associate Professor ~ \/ / /
~ Department of Biology ~ \ / /
~ New York University ~ [] / /
~ Main Building, Room 1009 ~ \ / /
~ 100 Washington Square East ~ \/ /
~ New York, NY 10003 ~ \ /
~ U S A ~ \/
~ Tel.: (212) 998-8254 ~ \
~ Fax: (212) 995-4015 ~ \
~ e-mail: david.fitch@nyu.edu ~
From: "Jennifer Gleason" <jgleason@ku.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 4:10 PM
Subject: Re: Other: experimental evolution computer programs
� Hi,
I know of a some programs that do some, but probably not all of what you are
looking for. They are available on the website for the Freeman & Herron
textbook, Evolutionary Analysis (http://wps.prenhall.com/esm_freeman_evol_3
). Once you enter the website, on the lefthand column is a link called
"Simulations." There you will find various simulations illustrating
different points. They are pretty good though the documentation is out of
date (it refers to the 2nd edition of the book, though if you are not using
the book, the references are irrelevant). I use the programs when I teach
Evolutionary Biology. Jon Herron wrote the programs and now he is
contributing to the EvoBeaker programs
http://www.simbio.com/fr_index.html?/EvoBeaker.html ) instead of developing
these more. EvoBeaker is very good, but it isn't free.
Cheers,
Jenny
----------
Dr. Jennifer Gleason
Assistant Professor
University of Kansas
Ecology and Evolutionary Biology
1200 Sunnyside Ave., Haworth Room 6006
Lawrence, KS 66045
785-864-5858
785-864-5321 (FAX)
jgleason@ku.edu
http://www.ku.edu/~eeb/faculty/gleason.html
____________________
From: "Renate Wesselingh" <wesselingh@ecol.ucl.ac.be>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 4:28 PM
Subject: Re: Other: experimental evolution computer programs
� Dear Else,
try EvoTutor http://www.evotutor.org/TutorA.html.
Best regards, Renate Wesselingh
-------------------
Renate A. Wesselingh
Unit� d'Ecologie et de Biog�ographie
Biodiversity Research Centre
Universit� catholique de Louvain
Croix du Sud, 4-5
B-1348 Louvain-la-Neuve
Belgium
phone: +32 10 473447 fax: +32 10 473490
e-mail: wesselingh@ecol.ucl.ac.be
From: "Daria Koscinski" <dkoscins@uwo.ca>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 5:27 PM
Subject: Re: Other: experimental evolution computer programs
� Hi,
I don't have any sure answers for you but I've been looking around
for evolution tutorials and found a couple of pages of interest. One
is from Ridley's Evolution textbook which has website resources - one
of which are virtual experiments. I can't try them since they are
only available for PC but they might be what you are looking for:
http://www.blackwellpublishing.com/ridley/experiments/
The site below has lots of lessons for various types of evolution
related questions:
http://www.indiana.edu/%7Eensiweb/home.html
Hope it helps. Good luck!
Daria Koscinski
From: "Jeremy M. Brown" <jembrown@mail.utexas.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Cc: <alemmon@evotutor.org>
Sent: Friday, September 08, 2006 5:41 PM
Subject: Re: Other: experimental evolution computer programs
� Else,
I'm not sure this is exactly what you're looking for, but try the website:
www.evotutor.org
It was written by a friend of mine and fellow graduate student here
at the Univ. of Texas-Austin, Alan Lemmon. It allows you to
manipulate most evolutionary parameters independently (but perhaps
not jointly?). I know this website is used in several evol. biol.
courses around the US.
Best,
Jeremy
� _____________________
From: "Bronwyn Heather Bleakley" <hbleakle@indiana.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 6:15 PM
Subject: RE: Other: experimental evolution computer programs
� Hi Else,
I've used PopG 2.0, which runs on windows and Mac to do exactly what you
want with students. It's written and distributed for free by Joe
Felsenstein at University of Washington. I copied the relevant information
from the website
(http://depts.washington.edu/genetics/courses/genet453/2002/) below for you.
--Heather
From: "Kirsten Fisher" <kirsten@pixelbiscuit.com>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 5:02 PM
Subject: Re: Other: experimental evolution computer programs
� Hi,
you might check out Evobeaker:
http://www.simbio.com/fr_index.html?/EvoBeaker.html
I think they have a demo you can order. In particular, the Columbine
exercise might be useful for you.
best wishes,
kirsten
_____________________________
From: "Paul Hohenlohe" <hohenlo@uoregon.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 8:11 PM
Subject: Re: Other: experimental evolution computer programs
Else-
I have used the Ecobeaker package of programs for teaching beginning
undergraduate students in an evolution course, and I would highly
recommend it. It has a number of ecological and evolutionary simulations
that are fairly user-friendly and visual. The same company also produces
"Evobeaker", an evolutionary package, that I have not used -- this may be
useful to you also. These can all be found at the website www.simbio.com
Good luck,
Paul
=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=<>=
Paul Hohenlohe, Postdoctoral Researcher
Department of Zoology
Oregon State University
Corvallis, OR 97331
Center for Ecology and Evolutionary Biology
University of Oregon
Eugene, OR 97403
hohenlo@uoregon.edu
ph: 541-760-9233 fax: 541-737-0501
From: "Yampolsky, Lev" <YAMPOLSK@mail.etsu.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Friday, September 08, 2006 7:54 PM
Subject: RE: Other: experimental evolution computer programs
Have you tried Populus (http://www.cbs.umn.edu/populus/)?
It's not ideal, but it certainly fits most of what you describe.
From: "kevin livingstone" <klivings@Trinity.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Saturday, September 09, 2006 6:52 PM
� Dear Else-
while not everything you might want, we have used the programs alleleA1
and popcycle that are a part of Freeman and Herron's evolution textbook
(but available for free) to demonstrate evolution to our undergraduate
classes.
cheers
-Kevin
popcycle:
http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849183-,00.html
alleleA1
http://wps.prenhall.com/esm_freeman_evol_3/0,8018,849255-,00.html
From: "Liam J. Revell" <ljrevell@artsci.wustl.edu>
To: <Else.Fjerdingstad@snv.jussieu.fr>
Sent: Sunday, September 10, 2006 5:59 PM
Subject: re: TeachingEvol.ComputerPrograms
� Dear Dr. Fjerdingstaf -
I have no idea if this is what you're looking for, but I used to have
available online a set of simple matlab functions to illustrate some
concepts in population genetics. The functions include:
- one that generates an animated cobweb plot and Wrightian fitness surface
for p(t) by p(t+1) for arbitrary genotypic fitnesses (specified by user),
- one that generates a cobweb plot for frequency dependent selection,
- one that simulates stochastic fertility selection,
- one that plots the erosion of LD while simulating the erosion of LD and
comparing it to the prediction,
- one that plots 3D fitness surfaces under various forms of epistasis
(e.g., ad x ad, ad x dom).
- one that simulates and animates the process of genetic drift,
- one that simulates the coalescent process,
- and several others.
Although I took the page down while I update my website, you can still get
to it by going to http://iguana.wustl.edu/~liam/evol_theory/matlab/ and
following the link to the old page.
Matlab (http://www.mathworks.com/products/matlab/) is both a high level
programming language and environment. My matlab functions might also run
in Octave (http://www.gnu.org/software/octave/) or SciLab
(http://www.scilab.org/), which are both open-source, free packages
(although many of the animated features might not work).
I hope this is of some help.
Liam
Liam Revell
Washington University, Department of Biology
web: http://iguana.wustl.edu/~liam/
email: ljrevell@artsci.wustl.edu
From: Alessia Guggisberg
To: Else.Fjerdingstad@snv.jussieu.fr
Sent: Monday, September 11, 2006 8:53 AM
Subject: Re: Other: experimental evolution computer programs
You may check the EvoTutor webpage ( http://www.evotutor.org/TutorA.html).
Dr. Else J. FJERDINGSTAD
Laboratoire d'Ecologie, CNRS UMR 7625
Universit� Pierre et Marie Curie
7 Quai St-Bernard, B�timent A, 7�me �tage, case 237
F-75252 Paris Cedex 05
FRANCE
Email: Else.Fjerdingstad@snv.jussieu.fr
T�l. +33 1 44 27 34 20, Fax. +33 1 44 27 35 16
Have a heart that never hardens, a temper that never tires
- Charles Dickens