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_, 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

login name should be:


and your password can be your email address.

You should then change directories

cd pub/thorne/

You should then get the file

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 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.