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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
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
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.
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.
234 results