Binary files Source code Manual

Phylogenetic motifs (PMs) predict protein functional site predictions from sequence alignments. Their predictive power has been demonstrated in many investigations, especially as applied to ligand-binding and active site regions.
The software miniMINER is a streamlined and self-contained tool for PM identification.
Download the complete package
  Files to download
You can access the redistributable file list in sourceforge file list or use the following direct links: The latest versions of source files are available via sourceforge subversion and can be browsed in its repository browser.
  A common miniMINER example
The most common use of miniMINER is to calculate phylogenetic similarity scores (PSZ) that quantify phylogenetic similarity; more negative scores indicate greater similarity. miniMINER outputs a PSZ score for each window of an input alignment using the following syntax:

java -jar miniminer-1.2.0.jar -m [options] inputfile

The options are described fully within the user’s manual. Note that webMINER, which includes several data visualization options, can be accessed at:
  • La D, Sutch B, Livesay DR (2005). Predicting protein functional sites with phylogenetic motifs. Proteins, 58:309-320.
  • Roshan U, Livesay DR, La D (2005). Improved phylogenetic motif identification using parsimony. Fifth IEEE Symposium on Bioinformatics and Bioengineering, BIBE05:19-26.
  • La D, Livesay DR (2005). Accurate functional site prediction using an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics, 6:116.
  • La D, Livesay DR (2005). MINER: software for phylogenetic motif identification. Nucleic Acids Research, 33:W267-W270.
  • KC DB, Livesay DR (2008). Improving position specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics, 24:2308-2316.
  • KC DB, Livesay DR. Topology improves phylogenetic motif functional site predictions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, In press.
  Last updated: 3/9/210