# How to Cite

## Cite PANORAMA

If you use PANORAMA in your research, please cite:

> Arnoux J, Mainguy J, Bry L, Fernandez de Grado Q, Hoblos Y, Vallenet D, Calteau A.
> **Panorama: a robust pangenome-based method for predicting and comparing biological systems across species.**
> *bioRxiv* 2025.12.22.695875; doi: [https://doi.org/10.64898/2025.12.22.695875](https://doi.org/10.64898/2025.12.22.695875)

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## Cite PPanGGOLiN

PANORAMA is built on top of [PPanGGOLiN](https://github.com/labgem/PPanGGOLiN). Please also cite:

> Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Médigue C, Calteau A, Cruveiller S, Mateus C, Gaspin C, Vallenet D, Mariadassou M.
> **PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.**
> *PLOS Computational Biology* 16(3): e1007732 (2020); doi: [https://doi.org/10.1371/journal.pcbi.1007732](https://doi.org/10.1371/journal.pcbi.1007732)

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## Cite PPanGGOLiN tools used by PANORAMA

Depending on which features you use, additional citations may be appropriate.

### Genomic islands (RGPs / spots)

If you use PANORAMA to study genomic islands, please also cite:

> Bazin A, Gautreau G, Médigue C, Vallenet D, Calteau A.
> **panRGP: a pangenome-based method to predict genomic islands and explore their diversity.**
> *Bioinformatics*, Volume 36, Issue Supplement_2, December 2020, Pages i651–i658; doi: [https://doi.org/10.1093/bioinformatics/btaa792](https://doi.org/10.1093/bioinformatics/btaa792)

### Modules

If you use PANORAMA to study modules, please also cite:

> Bazin A, Vallenet D, Calteau A.
> **panModule: detecting conserved modules in the variable regions of a pangenome graph.**
> *bioRxiv* 2021.12.06.471380; doi: [https://doi.org/10.1101/2021.12.06.471380](https://doi.org/10.1101/2021.12.06.471380)