From 5a6dacb8f8e5380cf8ef49cf9d2b918077c56803 Mon Sep 17 00:00:00 2001
From: Alexis  CRISCUOLO <alexis.criscuolo@pasteur.fr>
Date: Tue, 11 Jun 2019 10:42:56 +0200
Subject: [PATCH] Update README.md

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 README.md | 3 +++
 1 file changed, 3 insertions(+)

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 _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
 
@@ -194,6 +195,8 @@ As the basename was set to 'klebsiella', _JolyTree_ writes in few minutes the fo
 
 ## 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).
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