6. Citation & Funding

Citation

If you run ReporTree, please cite the publication:
Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V (2023) ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Medicine. doi: 10.1186/s13073-023-01196-1

Also, ReporTree relies on the work of other developers. So, depending on the functionalities you use, there are other tools that you must cite:

1. Grapetree: http://www.genome.org/cgi/doi/10.1101/gr.232397.117 (if you requested a grapetree analysis)
2. TreeCluster: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705769/pdf/pone.0221068.pdf (if you provided a newick tree)
3. vcf2mst: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08112-0 (if you provided a vcf or a list of variants)
4. ComparingPartitions: https://journals.asm.org/doi/10.1128/jcm.02536-05?permanently=true (if you requested "stability_regions")
5. Adjusted Wallace and cluster stability: https://www.biorxiv.org/content/10.1101/299347v1 (if you requested "stability_regions")
6. Ete3: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116/pdf/msw046.pdf (if you provided a newick tree)
7. cgmlst-dists: https://github.com/tseemann/cgmlst-dists
8. snp-sites: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056 (if you provided a multi-sequence alignment)

Funding

This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme.