response to info request for genetic programs

R.E. Hickson RHickson at massey.ac.nz
Sun Jun 13 00:57:11 EST 1993


Hello

a couple of weeks ago I posted a request for information on programs
illustrating genetic drift and basic phylogenetic reconstruction
principles for use in undergraduate teaching. I had several responses
and expressions of interest. Sorry for the delay in posting the results.
I hope the respondents don't mind my displaying some of their
comments/ideas here.

From:
      Joe Felsenstein,
      Dept. of Genetics, Univ. of Washington, Seattle, WA 98195
 Internet:         joe at genetics.washington.edu     (IP No. 128.95.12.41)
 Bitnet/EARN:      felsenst at uwavm

You can fetch by anonymous ftp a DOS program (including Turbo Pascal
source and executable) "illustrating genetic drift" from
directory  pub/popgen on my machine evolution.genetics.washington.edu

I think for phylogenies you will end up using PHYLIP together with (say)
CLUSTAL, but then I might be biased.

++++++++++++++++++++++++++++++

From: GILLESPIE at BIOLOGY.UTAG.EDU
		
 you could use the Pileup program that is found
in the GCG package.  The Pileup program uses a clustering method to
align
sequences that it is given.  This clustering is represented in a
dendrogram
that the program will save to a <.figure> file.  They are very careful
to
point out that this dendrogram is not a phylogenetic tree, and it is
not,
but the lengths of the branches are proportional to the similarity of
the
sequences.  Perhaps it is a place to start.

If you like Macintosh type stuff, a suite of programs are put out by a
company called DnaStar.  Under the program MegAlign the same type of
options are availible as those described above, though they call their
dendrograms phylogenys.  There sequence editing programs availible as
well
as other options that might give a student a pretty good walk through on
how phylogenys are constructed from entering the sequence, to using
different methods of alignment.

++++++++++++++++++++++++++++++

From: ebo at algodones.unm.edu ((E.A. Bouffier - John David))

  About 2 months ago I started working on a program for my genetic
algorithms
class. Since I wanted to model the biological processes more acurately,











I
started out by by trying to reproduce some of the simpler experiments of
Mendel and Morgan. I allowed the instructer/user to define the genome
from
a basic sequence to euploidic organisms. Being a GA (genetic algorithm),
I needed to keep track of the genetic drift of the population,
manipulate
the frequency of mutations for each gene (but not the timing), define
random
and non-random populations, and calculate map distances and linkage.

  To be honest, I was more interestred in applying what I refered to as
macro-mutations like "jumping genes", chromosomal non-disjunction,
horizantal
transfer of DNA through virusses, and euploidic events to my GA's.
In designing the original software, I set it up so that it could be used
as
a basis for several 2'nd year genetics lab simulations. I am planning to
continue playing with the idea, but my plate will be filling up very
quickly
since I may be seting up a database for the universities herbarium this
summer.
I could probably be presuaded to add some of the functionality that you
are
looking for, particularly if you could answer some questions I have
concerning some of the processes.

The current state of the software is a bit of a mess (I am some what
embarrassed to say). This was my first program in C++, though I have
programmed in C for some 12 years. Because of this I will be redesigning
it from scratch, and learning yet more of this enw language. I would be
interested in hearing back from you.

John Relethford may have more ideas about software as well. He's a
POPULUS
fan. His address is:

in%"relethjh at snyoneva.cc.oneonta.edu"

+++++++++++++++++++++++++++++++

From:	SOUSLEY at utkvx.utk.edu

I have POPULUS, and can send it as a self-extracting ZIP file on one
disc.

Or, I just found this in the populus directory:
    In addition to this brief read.me, the Populus disk contains 4 files
as
follows:

1) Populus.doc is an ascii text file that explains features and
requirements of
the software, many of which are new to this current version.  We suggest
that











you read it before using the program.  Note that full documentation is
an
internal part of Populus, accessible from the main help menu (press <F1>
once,
or twice depending on context), and that many program features are
adjusted
from the Options Menu (press <Alt-O>).

2) Populus.exe is the binary executable file that runs our program; it
should
be placed (with populus.ovr and populus.txt) in the hard-drive directory
that
you will use when running Populus.

3) Populus.ovr contains the overlays that swap different models and
routines in
and out of computer memory.  This file is required to run the program.

4) Populus.txt contains all of the indexed text screens that are
displayed by
Populus.  It is the last of three files (also populus.exe, populus.ovr)
that
are required to run the program.

     Populus allows you to save other files to disk.  For example, if
you elect
to preserve any of the configuration information chosen from the Populus
options menu, the program will save a populus.cfg file and your
configuration
will be loaded automatically each time Populus starts.  Parameter sets,
print
files, and data outputs may also be saved with filenames (*.par, *.prn
and
*.dat) of your choosing, but only the populus.exe, populus.ovr, and
populus.txt files are necessary to run the program.

     In today's viral climate I am no longer willing to distribute
software
that I cannot personally control; for this reason, I have not included a
compressed, self-extracting copy of Populus accessible from 360K 5.25"
disk
drives.  If you need to use a 360K drive, compress the Populus.ovr file
to fit, using a compression utility from the public domain or commercial
market.

     We encourage you to give this software without charge to any
students or
colleagues who will put it to good use.  When you do so, please pass on
the
entire 5-file package intact.  File sizes should be as follows:

                   populus.doc       8390 bytes
                   populus.exe     151952 bytes
                   populus.ovr     641968 bytes
                   populus.txt     352781 bytes











                   read.me           2767 bytes

If the file sizes that you receive differ from these values, your disk
is
corrupt and should be destroyed.  For $10 payable to the University of
Minnesota you can obtain a clean, up-to-date copy from Don Alstad,
Department
of Ecology, Evolution and Behavior, University of Minnesota, 318 Church
St. SE, Minneapolis 55455-0302.

It is available by anonymous ftp at ecology.ecology.umn.edu in the
pub/populus directory.  It may serve some of your needs.

+++++++++++++++++++++++++++++++

From:
      John R. Jungck, Biology, Beloit College
        jungck at beloit.edu

I am delighted to see someone who shares so many interests.  I am the
co-author of an educational simulation entitled the Microbial Genetics
Construction Kit which is good at replica plating (auxanography and
antibiotic sensitivity/resistance analysis and data collection
matrices),
serial dilution,  complementation, and conjugation (with two different
mathematical models of recombination, one being a simpler time of entry
model).  We have long wanted to put in Luria-Delbruck but have not to
date.
I know of one computer program for analyzing L-D experiments; it is by
Frank
Stewart in Applied Mathematics at Brown Univ. in Providence, RI - it is
called DataFit and runs on a Mac as does ours.

Frank Price and Virginia Vaughan wrote a fine population genetics
package
called Evolve.  It does a nice job with genetic drift because students
can
plot out population size as a function of generation number as well as
genotypic and allelic frequency plots.

Both Evolve and the Microbial Genetics Construction Kit are available on
the
BioQUEST Library (a CD).  You can contact the publisher at
asdg at umdd.umd.edu
or get a newsletter from bioquest at beloit.edu or get the address for
downloading a demo.

I use MacClade, PAUP, PHYLIP, and NT-SYS.  I frankly find that using
MacClade works well with students, especially since their data entry
interface improved in the formally published 3.0 edition.  We regular
use it
not only with undergraduates but also in workshops with high school
teachers
and have heard back reports from them about their use with hs students.












I believe that Tom Manney in the Physics dept at Kansas State is
building a
program on a PC to study UV sensitivity of yeast cells.  I should follow
up
on this if you don't find success.

+++++++++++++++++++++++++++++++

Note: I tried e-mailing bioquest at beliot.edu for the address for a demo
but received no reply.

Thanks once again for those who responded. Any more suggestions for
teaching basic genetic principles to undergraduates (particularly some
of the so-called classic experiments) are eagerly sought.


Regards

Robert Hickson
Molecular Genetics Unit
Massey University
New Zealand.



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