These programs are in .tar.gz archives containing documentation in README.txt
files. Download the archive you want, extract the files and read the README.txt file
(of course, you are also allowed to read the other files).
Under Windows, you will perhaps need a program like 7-zip to extract the files.
In a unix-like command-line environnement (like the Terminal you have in MacOSX
or Linux), go to the directory where you downloaded the archive (with the
command cd) and use tar:
tar -xvzf *.tar.gz
Other extraction tools might work.
Warning: these programs are not maintained. Bugs have been found in rely.py
If you are interested in running my repetition index method, you may write me
and we can think about making a new and less buggy version of the program.
The following programs should work on any computer on which a version of
python 2.3 to 2.7 is installed.
They are released under the GNU General Public Licence, version 2.
concatnexus.py and rely.py
concatnexus.py:
a program to prepare phylogenetic analyses using the partial combination approach
(Dettaï and Lecointre, 2004).
Can also be used to just assemble data matrices together.
rely.py:
a program to extract reliable clades from compared trees using the repetition index
(Li et al., 2010).
The use of rely.py is easier if you prepared your analyses with
concatnexus.py.
As of November 2010, the output format of MrBayes seems to have changed relative to the time I wrote the programs.
Some work may be needed in order to take this into account.
Some bugs affecting analyses where only some of the combinations are used have
been fixed in revision 19 of rely.py (uploaded September the 10th, 2009).
supertri.py
supertri.py:
a program implementing a supertree method based on branch support analyses of multiple independent data
sets (SuperTRI, Ropiquet et al., 2009).
Some bugs have been fixed in revision 57 of supertri.py (uploaded february the 12th, 2010).
I worked on an update to accomodate new input formats and to run with python 3 up until 2019 here.
Another updated 2024 version compatible with python 3 is available here. As of 2024, this is the "official" version.
As part of my work, I have made some code available on bitbucket.