From 6eef85fbd5f8b7868c65b3f389d3cfef72087da9 Mon Sep 17 00:00:00 2001 From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr> Date: Wed, 21 Feb 2024 15:37:25 +0100 Subject: [PATCH] 0.1 --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 671110f..a58c172 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ # LINtree -_LINtree_ is a command line tool written in [Java](https://docs.oracle.com/en/java/) to infer prefix trees with branch lengths from sets of Life Identification Number (LIN) codes (Vinatzer et al. 2017; Tian et al. 2020). +_LINtree_ is a command line tool written in [Java](https://docs.oracle.com/en/java/) to infer prefix trees with branch lengths from sets of Life Identification Number (LIN) codes (Marakeby et al. 2014; Vinatzer et al. 2017; Tian et al. 2020). Such LIN-based prefix trees are very useful to reflect the (phylogenetic) relationships among the encoded genomes (e.g. Hennart et al. 2022). @@ -99,6 +99,8 @@ The prefix tree (_Kp.nwk_) returned by _LINtree_ from the input file (_Kp.txt_) Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S (2022) _A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains._ **Molecular Biology and Evolution**, 39(7):msac135. [doi:10.1093/molbev/msac135](https://doi.org/10.1093/molbev/msac135) +Marakeby H, Badr E, Torkey H, Song Y, Leman S, Monteil CL, Heath LS, Vinatzer BA (2014) _A System to Automatically Classify and Name Any Individual Genome-Sequenced Organism Independently of Current Biological Classification and Nomenclature._ **PLoS ONE**, 9(2):e89142. [doi:10.1371/journal.pone.0089142](https://doi.org/10.1371/journal.pone.0089142) + Tian L, Huang C, Mazloom R, Heath LS, Vinatzer BA (2020) _LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa._ **Nucleic Acids Research**, 48(W1):W529-W537. [doi:10.1093/nar/gkaa190](https://doi.org/10.1093/nar/gkaa190) Vinatzer BA, Tian L, Heath LS (2017) _A proposal for a portal to make earth’s microbial diversity easily accessible and searchable._ **Antonie van Leeuwenhoek**, 110(10):1271-1279. [doi:10.1007/s10482-017-0849-z](https://doi.org/10.1007/s10482-017-0849-z) -- GitLab