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On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo.
Rabier CE, Berry V, Stoltz M, Santos JD, Wang W, Glaszmann JC, Pardi F, Scornavacca C. Rabier CE, et al. Among authors: berry v. PLoS Comput Biol. 2021 Sep 3;17(9):e1008380. doi: 10.1371/journal.pcbi.1008380. eCollection 2021 Sep. PLoS Comput Biol. 2021. PMID: 34478440 Free PMC article.
Representing a set of reconciliations in a compact way.
Scornavacca C, Paprotny W, Berry V, Ranwez V. Scornavacca C, et al. Among authors: berry v. J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28. J Bioinform Comput Biol. 2013. PMID: 23600816 Free article.
SylvX: a viewer for phylogenetic tree reconciliations.
Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V. Chevenet F, et al. Among authors: berry v. Bioinformatics. 2016 Feb 15;32(4):608-10. doi: 10.1093/bioinformatics/btv625. Epub 2015 Oct 29. Bioinformatics. 2016. PMID: 26515823
PhySIC: a veto supertree method with desirable properties.
Ranwez V, Berry V, Criscuolo A, Fabre PH, Guillemot S, Scornavacca C, Douzery EJ. Ranwez V, et al. Among authors: berry v. Syst Biol. 2007 Oct;56(5):798-817. doi: 10.1080/10635150701639754. Syst Biol. 2007. PMID: 17918032
RecPhyloXML: a format for reconciled gene trees.
Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V. Duchemin W, et al. Among authors: berry v. Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389. Bioinformatics. 2018. PMID: 29762653 Free PMC article.
Quartets and unrooted phylogenetic networks.
Gambette P, Berry V, Paul C. Gambette P, et al. Among authors: berry v. J Bioinform Comput Biol. 2012 Aug;10(4):1250004. doi: 10.1142/S0219720012500047. Epub 2012 Jun 22. J Bioinform Comput Biol. 2012. PMID: 22809417 Free article.
Multipolar consensus for phylogenetic trees.
Bonnard C, Berry V, Lartillot N. Bonnard C, et al. Among authors: berry v. Syst Biol. 2006 Oct;55(5):837-43. doi: 10.1080/10635150600969880. Syst Biol. 2006. PMID: 17060203
234 results