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Commit 6eef85fb authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO :black_circle:
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# LINtree # 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). 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_) ...@@ -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) 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) 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) 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)
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