_JolyTree_ (named in memory of [Nicolas Joly](https://research.pasteur.fr/en/member/nicolas-joly/)) is a command line script written in [Bash](https://www.gnu.org/software/bash/) that allows a distance-based phylogenetic tree with branch supports to be quickly inferred from non-aligned genome sequences.
_JolyTree_ runs on UNIX, Linux and most OS X operating systems.
For more details, see the associated publication (Criscuolo 2019).
## Installation and execution
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## References
Criscuolo A (2019) A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies. Research Ideas and Outcomes, 5:e36178. [doi:10.3897/rio.5.e36178](https://riojournal.com/article/36178/).
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6):368-376. [doi:10.1007/BF01734359](https://link.springer.com/article/10.1007/BF01734359).
Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Molecular Biology and Evolution, 32(10):2798-2800. [doi:10.1093/molbev/msv150](https://doi.org/10.1093/molbev/msv150).
