IPK: Inference of Phylo-K-mers

Please cite: [1]

IPK is a tool for computing phylo-k-mers for a fixed phylogeny.

For more information about phylo-k-mers, see our papers: one, two, three.

If you want to experiment with phylo-k-mers and write some code, check out our examples to see how to use the code of IPK.

Rapid installation via Bioconda

It is advised to install the package in a new environment, because our C++ dependencies are strict and may clash with other packages requiring, for instance, libboost. We also recommend to use `mamba, which is more faster in solving environment dependencies.

conda create -n my_env
conda activate my_env
conda config --set channel_priority strict
mamba install ipk

References

[1] Romashchenko, Nikolai et al. EPIK: precise and scalable evolutionary placement with informative k-mers. Bioinformatics, 39.12 (2023), btad692.

[2] Romashchenko, Nikolai. Computing informative k-mers for phylogenetic placement. Diss. Université Montpellier, 2021.

[3] Linard, Benjamin et al. “Rapid alignment-free phylogenetic identification of metagenomic sequences.” Bioinformatics 35.18 (2019): 3303-3312.

[4] Scholz, Guillaume E., et al. “Rapid screening and detection of inter-type viral recombinants using phylo-k-mers.” Bioinformatics 36.22-23 (2020): 5351-5360.