Computing Phylo-$k$-Mers

Autor: Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi

Publikováno v: IEEE/ACM Transactions on Computational Biology and Bioinformatics. :1-9

Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and assuming a phylog

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f920dc8e8b54b28e4eac2cc260308d6d
https://doi.org/10.1109/tcbb.2023.3278049

PEWO: a collection of workflows to benchmark phylogenetic placement

Autor: Nikolai Romashchenko, Fabio Pardi, Benjamin Linard, Eric Rivals

Publikováno v: Bioinformatics
Bioinformatics, 2020, 36 (21), pp.5264-5266. ⟨10.1093/bioinformatics/btaa657⟩
Bioinformatics, Oxford University Press (OUP), In press, ⟨10.1093/bioinformatics/btaa657⟩

Motivation Phylogenetic placement (PP) is a process of taxonomic identification for which several tools are now available. However, it remains difficult to assess which tool is more adapted to particular genomic data or a particular reference taxonom

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8f12192df1674fd67475a636ded77274
https://pubmed.ncbi.nlm.nih.gov/32697844