The programs that inspire this web page are for studying rates of
evolution and for estimating divergence times. I had been
them via email because I wanted to emphasize to each and every
user that I realize they need a lot of improvement. But, this
a more time-efficient way to distribute them. Please contact me
thorne _at_ statgen.ncsu.edu, phone: 919-515-1946) with any comments,
In addition to documentation files that I have written and that I
with the multidivtime software, a helpful manual has been written by
Rutschmann (Institute of Systematic Botany, University of Zurich).
kindly allowed me to distribute his manual here.
The programs work with MAC OSX, linux, and other flavors of
also seem to work with the windows operating system but I can't
on this because I do not use them with the windows operating
Andrew Crawford of the Smithsonian Institution has generously posted
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
click here or
You should anonymous ftp to statgen.ncsu.edu
login name should be:
and your password can be your email address.
You should then change directories
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
in the appropriate directory and then type:
This should result in the creation of a directory named
lots of files. The file named "readme" should be one of
It is the first file to read after downloading.
III. Thanks to ...
These programs are the result of a highly collaborative
(University of Tokyo) and Jeff Thorne
State). In no particular order, a non-exhaustive list of the large
of other people who have provided valuable input is: Ian Painter,
Tae-Kun Seo, Stéphane Aris-Brosou, Ziheng Yang, Brian
Xiang, Masami Hasegawa, Cliff Cunningham, Mike Sanderson, Chris Smith, and Chris
Support for this work has been provided by the Japanese Science and
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
previous version of the multidivtime program of this software (i.e.,
version posted 8/5/03 and available until this version was posted on
The bug was inadvertently introduced by me when I wrote the 8/5/03
and is corrected in this 9/25/03 version. The bug would very likely cause
when data were analyzed with tree topologies that had multifurcations
in the ingroup. For tree topologies that were fully
in the ingroup, the previous version did not have any bugs of which I
aware. If you know researchers who may be using the immediately
version of this program, please suggest to them that they download
this version instead.