ATGC: IPK

IPK: Inference of Phylo-K-mers

Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi.

Computing Phylo-k-Mers. IEEE ACM Trans. Comput. Biol. Bioinform. 20(5): 2889-2897 (2023)

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

IPK takes as input

A set of reference sequences that are aligned in a FASTA file.
A rooted reference tree is inferred by Maximum Likelihood method, and in accordance with the alignment.

It yields a database of phylo-k-mers stored in binary file on your hard disk.
This file is a required input for EPIK, SHERPAS, etc.

Keywords

Indexing, k-mers, filtering, phylogenetic placement, metabarcoding, software, database, Divide-and-Conquer

For a detailed description, feel free to read the Open Access publication or to look at a video presentation made during a seminar at IRD.

Publication

EPIK: Precise and scalable evolutionary placement with informative k-mers
N. Romashchenko, B. Linard, F. Pardi, E. Rivals
Bioinformatics, in press
DOI: 10.1093/bioinformatics/btad692

IPK: Inference of Phylo-K-mers

IPK takes as input

Keywords

Publication

Links