MinPath

• MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.
• Reference: Yuzhen Ye and Thomas G. Doak. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Computational Biology, 2009, 5(8): e1000465 (paper link)(Supplementary material)
• Use the server
• Download the software
  • Latest version: 1.2 (download the package)
    • Add supports for any pathway system (in addition to KEGG and SEED).
    • What you need to provide? A pathway-function mapping file.
  • Older versions
    • Version 1.1 (download the package): Add outputs of detailed pathway assignments -- what functions are predicted in each pathway, and how many reads assigned to each function.
    • Version 1.0 (download the package)
• Instructions: how to install and use MinPath locally; how to read MinPath report
• Contact: Yuzhen Ye (yye@indiana.edu)