Merge pull request #32 from phylo42/nromashchenko-patch-1

Update README.md

README.md

@@ -1,18 +1,22 @@
 # IPK: Inference of Phylo-K-mers
 [![build](https://github.com/phylo42/IPK/actions/workflows/build.yml/badge.svg)](https://github.com/phylo42/IPK/actions/workflows/build.yml)
 
+**Please cite:**  [![doi](https://img.shields.io/static/v1?label=doi&message=10.1093/bioinformatics/btad692&color=blue)](https://doi.org/10.1093/bioinformatics/btad692) [1]
+
 IPK is a tool for computing phylo-k-mers for a fixed phylogeny.
 
 [Link to documentation](https://phylo-k-mers.readthedocs.io/) 
 
-For more information about phylo-k-mers, see our papers: [one](https://tel.archives-ouvertes.fr/tel-03629440/ "My thesis on phylo-k-mers for phylogenetic placement"),  [two](https://doi.org/10.1093/bioinformatics/btz068 "This paper introduced phylo-k-mers"), [three](https://doi.org/10.1093/bioinformatics/btaa1020 "Another paper that uses IPK and phylo-k-mers").
+For more information about phylo-k-mers, see our papers: [one](https://academic.oup.com/bioinformatics/article/39/12/btad692/7425449),  [two](https://doi.org/10.1093/bioinformatics/btz068), [three](https://doi.org/10.1093/bioinformatics/btaa1020).
 
 If you want to experiment with phylo-k-mers and write some code, check out our [examples](https://github.com/phylo42/I2L/tree/master/examples) to see how to use the code of IPK.
 
+
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+[1] Romashchenko, Nikolai et al. EPIK: precise and scalable evolutionary placement with informative k-mers. Bioinformatics, 39.12 (2023), btad692.
 
-[1] Romashchenko, Nikolai. Computing informative k-mers for phylogenetic placement. Diss. Université Montpellier, 2021.
+[2] Romashchenko, Nikolai. Computing informative k-mers for phylogenetic placement. Diss. Université Montpellier, 2021.
 
-[2] Linard, Benjamin, Krister Swenson, and Fabio Pardi. "Rapid alignment-free phylogenetic identification of metagenomic sequences." Bioinformatics 35.18 (2019): 3303-3312.
+[3] Linard, Benjamin et al. "Rapid alignment-free phylogenetic identification of metagenomic sequences." Bioinformatics 35.18 (2019): 3303-3312.
 
-[3] Scholz, Guillaume E., et al. "Rapid screening and detection of inter-type viral recombinants using phylo-k-mers." Bioinformatics 36.22-23 (2020): 5351-5360.
+[4] Scholz, Guillaume E., et al. "Rapid screening and detection of inter-type viral recombinants using phylo-k-mers." Bioinformatics 36.22-23 (2020): 5351-5360.