Multidivtime Software
The programs that inspire this web page are for studying rates of
molecular
evolution and for estimating divergence times. I had been
distributing
them via email because I wanted to emphasize to each and every
interested
user that I realize they need a lot of improvement. But, this
may be
a more time-efficient way to distribute them. Please contact me
(email:
thorne _at_ statgen.ncsu.edu, phone: 919-515-1946) with any comments,
questions,
or suggestions.
In addition to documentation files that I have written and that I
distribute
with the multidivtime software, a helpful manual has been written by
Frank
Rutschmann (Institute of Systematic Botany, University of Zurich).
He has
kindly allowed me to distribute his manual here.
The programs work with MAC OSX, linux, and other flavors of
unix. They
also seem to work with the windows operating system but I can't
comment much
on this because I do not use them with the windows operating
system.
Andrew Crawford of the Smithsonian Institution has generously posted
tips
and instructions for using the programs with Mac OSX.
Dr.Yoshinori Kumazawa of Nagoya University has impressively managed
to analyze amino acid sequences with a model of amino acid replacement
designed for mitochondrial proteins (mtREV-F) and with discrete
gamma rate heterogeneity among sites.
You can download code and notes
that he has shared by clicking here.
I. To download the
software,
click here or
You should anonymous ftp to statgen.ncsu.edu
login name should be:
anonymous
and your password can be your email address.
You should then change directories
cd pub/thorne/
You should then get the file multidistribute.09.25.03.zip
II. After getting the software
...
Either do whatever you normally do to files that you download or
...
If you are using MAC OSX or linux or unix, place the
multidistribute.09.25.03.zip
in the appropriate directory and then type:
unzip multidistribute.09.25.03.zip
This should result in the creation of a directory named
multidistribute with
lots of files. The file named "readme" should be one of
these.
It is the first file to read after downloading.
III. Thanks to ...
These programs are the result of a highly collaborative
research project
between Hirohisa
Kishino
(University of Tokyo) and Jeff Thorne
(N.C.
State). In no particular order, a non-exhaustive list of the large
number
of other people who have provided valuable input is: Ian Painter,
Bill Bruno,
Tae-Kun Seo, Stéphane Aris-Brosou, Ziheng Yang, Brian
Wiegmann, Jenny
Xiang, Masami Hasegawa, Cliff Cunningham, Mike Sanderson, Chris Smith, and Chris
Basten.
Support for this work has been provided by the Japanese Science and
Technology
Corporation and the U.S. National Science Foundation (Awards 9909348, 0077503, 0089745, 0120635, 0445180).
IMPORTANT NOTE: Thanks to Susanne Renner, a serious bug was found in
the
previous version of the multidivtime program of this software (i.e.,
the
version posted 8/5/03 and available until this version was posted on
9/25/03).
The bug was inadvertently introduced by me when I wrote the 8/5/03
version
and is corrected in this 9/25/03 version. The bug would very likely cause
problems
when data were analyzed with tree topologies that had multifurcations
somewhere
in the ingroup. For tree topologies that were fully
bifurcating
in the ingroup, the previous version did not have any bugs of which I
am
aware. If you know researchers who may be using the immediately
previous
version of this program, please suggest to them that they download
this version instead.