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APE: Analyses of Phylogenetics and Evolution in R language.
Paradis E, Claude J, Strimmer K. Paradis E, et al. Bioinformatics. 2004 Jan 22;20(2):289-90. doi: 10.1093/bioinformatics/btg412. Bioinformatics. 2004. PMID: 14734327
APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). ...
APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods fo …
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.
Popescu AA, Huber KT, Paradis E. Popescu AA, et al. Among authors: paradis e. Bioinformatics. 2012 Jun 1;28(11):1536-7. doi: 10.1093/bioinformatics/bts184. Epub 2012 Apr 11. Bioinformatics. 2012. PMID: 22495750
apex: phylogenetics with multiple genes.
Jombart T, Archer F, Schliep K, Kamvar Z, Harris R, Paradis E, Goudet J, Lapp H. Jombart T, et al. Among authors: paradis e. Mol Ecol Resour. 2017 Jan;17(1):19-26. doi: 10.1111/1755-0998.12567. Epub 2016 Aug 12. Mol Ecol Resour. 2017. PMID: 27417145 Free PMC article.
Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages.
Warren BH, Hagen O, Gerber F, Thébaud C, Paradis E, Conti E. Warren BH, et al. Among authors: paradis e. Evolution. 2018 Oct;72(10):2005-2024. doi: 10.1111/evo.13582. Epub 2018 Sep 11. Evolution. 2018. PMID: 30151822
Studies in insular environments have often documented a positive association of extinction risk and evolutionary uniqueness (i.e., how distant a species is from its closest living relative). ...
Studies in insular environments have often documented a positive association of extinction risk and evolutionary uniqueness (i.e., ho …
The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies.
Galewski T, Tilak MK, Sanchez S, Chevret P, Paradis E, Douzery EJ. Galewski T, et al. Among authors: paradis e. BMC Evol Biol. 2006 Oct 9;6:80. doi: 10.1186/1471-2148-6-80. BMC Evol Biol. 2006. PMID: 17029633 Free PMC article.
Random phylogenies and the distribution of branching times.
Paradis E. Paradis E. J Theor Biol. 2015 Dec 21;387:39-45. doi: 10.1016/j.jtbi.2015.09.005. Epub 2015 Sep 12. J Theor Biol. 2015. PMID: 26366932
Statistical analysis of diversification with species traits.
Paradis E. Paradis E. Evolution. 2005 Jan;59(1):1-12. Evolution. 2005. PMID: 15792222
Beyond the Mediterranean peninsulas: evidence of central European glacial refugia for a temperate forest mammal species, the bank vole (Clethrionomys glareolus).
Deffontaine V, Libois R, Kotlík P, Sommer R, Nieberding C, Paradis E, Searle JB, Michaux JR. Deffontaine V, et al. Among authors: paradis e. Mol Ecol. 2005 May;14(6):1727-39. doi: 10.1111/j.1365-294X.2005.02506.x. Mol Ecol. 2005. PMID: 15836645
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