CBiS Software

Software available for download or use is: PyEvolve Pozitiv GE Bi-Plot Chip Stability Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package.

PyEvolve

PyEvolve is an object-oriented toolkit designed to perform existing, and for the development of new, methods of molecular evolutionary analysis. The functional capabilities of PyEvolve are centered on its ability to perform phylogeny-based maximum-likelihood calculations. PyEvolve implements a range of existing and several novel Markov models of substitution (nucleotide, dinucleotide, codon, protein, and models for measuring interactions between sites) that can be used for these calculations.

Download COGENT, which includes PyEvolve, view the latest documentation, or send us a comment/query.

Publications and Presentations on PyEvolve:

• ISMB Poster 2003 Wakefield et al
• ISMB Poster 2003 Huttley et al
• Paper describing PyEvolve at BMC Bioinformatics
  

For more information contact Gavin Huttley.

Pozitiv

Pozitiv is a sequence database mining and alignment program. More details, including contact, may be found at:

http://datamining.anu.edu.au/software/pozitiv/index.html

The GE-biplot

The GE-biplot (gene expression biplot) is a useful method for exploratory analysis of microarray data that allows a visual appraisal of
both genes and samples.The R source code and documentation are available for download. For questions about this code, contact Yvonne Pittelkow.

Publications on the GE-biplot can be found from our Microarray Site.

Chip Stability

Bootstrap Principal Components Analysis is a method of evaluating chip stability. The R source code is available for download, as is a demo and the function documentation. For questions about this code, contact Yvonne Pittelkow.

Publications on the chip stability software can be found from our Microarray Site.

Vestige

Vestige is a maximum likelihood based phylogenetic footprinting application based on the PyEvolve molecular evolution toolkit.
Vestige compares the evolutionary distance calculated using maximum likelihood and uses variation in this length to identify regions that are unusually conserved.

• Vestige_MacOSX_Droplets.tar.gz
• Vestige.tar.gz
• http://www.biomedcentral.com/1471-2105/6/130/abstract

For more information contact vestige@cbis.anu.edu.au.