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
Links