IPK: Inference of Phylo-K-mers

IPK is a program for inference of phylo-k-mers. You will need to use IPK if you want to use any of the following:

1. Alignment-free phylogenetic placement with EPIK.

2. Detection of novel virus recombinants with SHERPAS.

3. Protein gene family classification with CLAPPAS.

4. Or do your own research experimenting with phylo-k-mers.

Check out the Installation and Getting started for general information. See Command line reference for detailed information about program options.

Warning

Although I2L (IPK’s Interface Library) is currently stable, it is still under development. Future updates of the library may not be backward compatible. This means that databases built with the current version of IPK may not be compatible with the future versions of phylo-k-mer-based tools (e.g., EPIK and SHERPAS). Check out the changelog for breaking changes.

Contents

• Installation
  • Install dependencies and build source code
  • Other dependencies
  • Check installation
• Getting started
  • I want a quick example
  • I want to read the docs
    • Reference multiple alignment
    • Reference phylogenetic tree
    • Ancestral reconstruction
      • Passing parameters via command line
      • Passing parameters via config file
    • K-mer size and score threshold
      • K-mer size
      • Score threshold
      • Recommendations
• Command line reference