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Items: 1 to 20 of 76


Fast and accurate branch lengths estimation for phylogenomic trees.

Binet M, Gascuel O, Scornavacca C, Douzery EJ, Pardi F.

BMC Bioinformatics. 2016 Jan 7;17:23. doi: 10.1186/s12859-015-0821-8.


Fast Dating Using Least-Squares Criteria and Algorithms.

To TH, Jung M, Lycett S, Gascuel O.

Syst Biol. 2016 Jan;65(1):82-97. doi: 10.1093/sysbio/syv068. Epub 2015 Sep 30.


A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK.

Mourad R, Chevennet F, Dunn DT, Fearnhill E, Delpech V, Asboe D, Gascuel O, Hue S; UK HIV Drug Resistance Database & the Collaborative HIV, Anti-HIV Drug Resistance Network.

AIDS. 2015 Sep 24;29(15):1917-25. doi: 10.1097/QAD.0000000000000768.


FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.

Lefort V, Desper R, Gascuel O.

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.


TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.

Nucleic Acids Res. 2015 Jul 1;43(W1):W3-6. doi: 10.1093/nar/gkv310. Epub 2015 Apr 8.


Mathematical and computational evolutionary biology (2013).

Gascuel O, Stadler T.

Syst Biol. 2015 Jan;64(1):1-2. doi: 10.1093/sysbio/syu086. No abstract available.


FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.

Dang CC, Le VS, Gascuel O, Hazes B, Le QS.

BMC Bioinformatics. 2014 Oct 24;15:341. doi: 10.1186/1471-2105-15-341.


Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

Ghouila A, Florent I, Guerfali FZ, Terrapon N, Laouini D, Yahia SB, Gascuel O, Bréhélin L.

PLoS One. 2014 Jun 5;9(6):e95275. doi: 10.1371/journal.pone.0095275. eCollection 2014.


Predicting the ancestral character changes in a tree is typically easier than predicting the root state.

Gascuel O, Steel M.

Syst Biol. 2014 May;63(3):421-35. doi: 10.1093/sysbio/syu010. Epub 2014 Feb 21.


Deep conservation of human protein tandem repeats within the eukaryotes.

Schaper E, Gascuel O, Anisimova M.

Mol Biol Evol. 2014 May;31(5):1132-48. doi: 10.1093/molbev/msu062. Epub 2014 Feb 3.


Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner.

Frange P, Meyer L, Jung M, Goujard C, Zucman D, Abel S, Hochedez P, Gousset M, Gascuel O, Rouzioux C, Chaix ML; ANRS PRIMO Cohort Study Group.

PLoS One. 2013 Jul 9;8(7):e69144. doi: 10.1371/journal.pone.0069144. Print 2013.


The behavior of admixed populations in neighbor-joining inference of population trees.

Kopelman NM, Stone L, Gascuel O, Rosenberg NA.

Pac Symp Biocomput. 2013:273-84.


Searching for virus phylotypes.

Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O.

Bioinformatics. 2013 Mar 1;29(5):561-70. doi: 10.1093/bioinformatics/btt010. Epub 2013 Jan 17.


Computational discovery of regulatory elements in a continuous expression space.

Lajoie M, Gascuel O, Lefort V, Bréhélin L.

Genome Biol. 2012 Nov 27;13(11):R109. doi: 10.1186/gb-2012-13-11-r109.


Combinatorics of distance-based tree inference.

Pardi F, Gascuel O.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16443-8. doi: 10.1073/pnas.1118368109. Epub 2012 Sep 25.


Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Terrapon N, Gascuel O, Maréchal E, Bréhélin L.

BMC Bioinformatics. 2012 May 1;13:67. doi: 10.1186/1471-2105-13-67.


Modeling protein evolution with several amino acid replacement matrices depending on site rates.

Le SQ, Dang CC, Gascuel O.

Mol Biol Evol. 2012 Oct;29(10):2921-36. Epub 2012 Apr 6.


The origin and evolutionary history of HIV-1 subtype C in Senegal.

Jung M, Leye N, Vidal N, Fargette D, Diop H, Toure Kane C, Gascuel O, Peeters M.

PLoS One. 2012;7(3):e33579. doi: 10.1371/journal.pone.0033579. Epub 2012 Mar 28.


Branch lengths on birth-death trees and the expected loss of phylogenetic diversity.

Mooers A, Gascuel O, Stadler T, Li H, Steel M.

Syst Biol. 2012 Mar;61(2):195-203. doi: 10.1093/sysbio/syr090. Epub 2011 Aug 24.


ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

Dang CC, Lefort V, Le VS, Le QS, Gascuel O.

Bioinformatics. 2011 Oct 1;27(19):2758-60. doi: 10.1093/bioinformatics/btr435. Epub 2011 Jul 26.

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