A tool for reference-free phylogeny

In this repository, you might find source codes for the reference-free phylogeny presented in the paper:

Petr Ryšavý, Filip Železný
Reference-Free Phylogeny from Sequencing Data
BioData Mining 16, 13 (2023). https://doi.org/10.1186/s13040-023-00329-x

Aim of this tool is to calculate distance matrix between several genomes knowing only raw read data and/or contig assemblies. The method is based on extension of the Monge-Elkan distance.

To run the method yourself, download the relase bundle from the relase, have Java installed on your system (source codes were compiled using Java 11), and run on the attached simple dataset using commad

java -cp reference-free-phylogeny.jar rysavpe1.reads.cli.Main -c testdata/contigs/* -r testdata/reads/* -o distanceMatrix.dat -d 3

The distance matrix is then printed to the distanceMatrix.dat file.