research publications software other stuff contact

I have developed a number of bioinformatics applications, some of which are available here. More are available on Andrew Roger's software site; they tend to be less well maintained, but feel free to contact me if you have any trouble getting them to work.

PopART

My population genetics software, PopART, is now hosted on its own website: popart.otago.ac.nz. Please go there to download the latest version of PopART or to view documentation and screenshots.

Conclustador

This is the method described in our 2011 MBE paper. This is a clustering-based method for assessing congruence in very large phylogenomic datasets. This is very much an alpha-test version. Please contact me if you want to use this program, as the output is rather hard to decipher, and the program itself may be difficult to compile (requires a working installation of LAPACK).

Concaterpillar

This application is described in our 2004 Systematic Biology paper. This is a hierarchical likelihood-ratio test for phylogenetic congruence. There is more information about the version history via Andrew Roger's site, and a somewhat outdated README file, but this is the latest version. You can run it with the -h flag to get a usage message.

NEW: Concaterpillar 1.8a now uses mpi4py instead of PyMPI. It also works with RAxML 7.3. Please try it out and let me know if you find any bugs!

Note that Concaterpillar 1.7.x and earlier will not work with versions of RAxML newer that 7.2.

Windows users: Concaterpillar was developed with Mac OSX and Linux/Unix users in mind. If you don't have access to either of these operating systems, you can download Concaterpillar 1.4 for Windows. If I get enough requests, I'll consider porting newer versions over to Windows.

IMPORTANT FOR MPI USERS: Version 1.7 had some mpi4py flags, which was a mistake. The latest "stable" version (1.7.2) uses PyMPI. If you have mpi4py installed, but not the ancient PyMPI, try version 1.8a (which may have some bugs that I haven't spotted). Thanks to Kevin Kocot and Scott Santos for pointing this out.

GenomeCentral

The methods described in our 2010 PNAS paper for assessing network centralities among genomes and mobile elements has been implemented in a series of Python scripts and C programs. These are available by request only.

MCMC simulation software:

This software is described in a manuscript that has not yet been published. Please contact me if you download it. The domestication code is my implementation of the model described in Allaby et al (2008). mcmctools is a Python module for running MCMC-based simulations as described in our manuscript.