CNIDARIA: fast, reference-free phylogenomic clustering
[https://travis-ci.org/sauloal/cnidaria](
Manual & Wiki: https://github.com/sauloal/cnidaria/wiki
Cnidaria does not need to be compiled but if you really want to, please refer to INSTALL.md.
Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.
Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.
Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria
Contact: [email protected]