Research Software

Software

The software presented here are small utility programs created in order to extend functionality of available software such as PAUP*, r8s, and MrBayes and to simplify some of the more tedious analyses.

Initially some were made using HyperCard (for the Macintosh) but recent versions are written in Perl which is free and already installed on Mac OS X and other Unix/Linux distributions. It is available for all relevant platforms.
My programs are supplied as binhexed self-extracting archives or gzipped tar archives.
Some of the utilities output trees for convenient viewing and printing using Rod Page's TreeView program.

Send bug reports to:
Bug reports should include program version, information about platform, detailed description of the problem and relevant files if you want me to investigate the problem.

AutoDecay - Helps calculating decay indices (also known under various other names). See Bremer (Evolution 42:795-803. 1988; Cladistics 10(3):295-304. 1994) and Donoghue et al. Ann. Missouri Bot. Gard. 79(2):333-345. 1992). AutoDecay uses reverse constraints in PAUP*.

The latest version of AutoDecay (5.06) currently works with PAUP* 4.0. It is written in Perl and can be run on most platforms. This is the currently supported version. It has a command line interface and should run on almost anything. I have used it on Linux and Darwin/Mac OS X, but I've had reports from people that have used it on Windows as well as Mac OS9 (MacPerl). Some tweaking is necessary for Mac OS9.
Before downloading, please check out the README file.
Also, if you are uncomfortable with the command line, there is additional help available.
Please email me if you need old hypercard versions for the Mac.

The r8s bootstrap kit helps performing bootstraps in Mike Sanderson's r8s program.
It consists of a number of Perl scripts and three general command blocks for use with PAUP* and r8s. Also, there's a pretty detailed step-by-step description. Includes info on NPRS as well as PL bootstraps.

MrBayes tree file scanners - These two Perl scripts can be used with MrBayes (versions 2.01 and 3).

* mbscan, scans an output parameter file (".p") for the best sample(s) and puts the corresponding tree(s) in a separate #NEXUS tree file.
* treefilter, scans an output tree file (".t") and selects only those trees which contain a specified node.