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Items: 1 to 20 of 27

1.

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.

Bioinformatics. 2016 Feb 26. pii: btw105. [Epub ahead of print]

PMID:
27153713
2.

A Resolution of the Static Formulation Question for the Problem of Computing the History Bound.

Matsieva J, Kelk S, Scornavacca C, Whidden C, Gusfield D.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Feb 11. [Epub ahead of print]

PMID:
26887004
3.

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.

4.

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality.

To TH, Jacox E, Ranwez V, Scornavacca C.

BMC Bioinformatics. 2015 Nov 14;16:384. doi: 10.1186/s12859-015-0803-x.

5.

SylvX: a viewer for phylogenetic tree reconciliations.

Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V.

Bioinformatics. 2016 Feb 15;32(4):608-10. doi: 10.1093/bioinformatics/btv625. Epub 2015 Oct 29.

PMID:
26515823
6.

Efficient algorithms for reconciling gene trees and species networks via duplication and loss events.

To TH, Scornavacca C.

BMC Genomics. 2015;16 Suppl 10:S6. doi: 10.1186/1471-2164-16-S10-S6. Epub 2015 Oct 2.

7.

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.

Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C, McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D808-18. doi: 10.1093/nar/gkv966. Epub 2015 Sep 29.

8.

Inferring gene duplications, transfers and losses can be done in a discrete framework.

Ranwez V, Scornavacca C, Doyon JP, Berry V.

J Math Biol. 2016 Jun;72(7):1811-44. doi: 10.1007/s00285-015-0930-z. Epub 2015 Sep 4.

PMID:
26337177
9.

Reconstructible phylogenetic networks: do not distinguish the indistinguishable.

Pardi F, Scornavacca C.

PLoS Comput Biol. 2015 Apr 7;11(4):e1004135. doi: 10.1371/journal.pcbi.1004135. eCollection 2015 Apr.

10.

Exploring the space of gene/species reconciliations with transfers.

Chan YB, Ranwez V, Scornavacca C.

J Math Biol. 2015 Nov;71(5):1179-209. doi: 10.1007/s00285-014-0851-2. Epub 2014 Dec 14.

PMID:
25502987
11.

Joint amalgamation of most parsimonious reconciled gene trees.

Scornavacca C, Jacox E, Szöllősi GJ.

Bioinformatics. 2015 Mar 15;31(6):841-8. doi: 10.1093/bioinformatics/btu728. Epub 2014 Nov 6.

12.

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees.

van Iersel L, Kelk S, Lekić N, Scornavacca C.

BMC Bioinformatics. 2014 May 5;15:127. doi: 10.1186/1471-2105-15-127.

13.

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.

Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V.

Mol Biol Evol. 2014 Jul;31(7):1923-8. doi: 10.1093/molbev/msu132. Epub 2014 Apr 9.

14.

Reconciliation-based detection of co-evolving gene families.

Chan YB, Ranwez V, Scornavacca C.

BMC Bioinformatics. 2013 Nov 20;14:332. doi: 10.1186/1471-2105-14-332.

15.

Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods.

Nguyen TH, Ranwez V, Berry V, Scornavacca C.

PLoS One. 2013 Oct 4;8(10):e73667. doi: 10.1371/journal.pone.0073667. eCollection 2013.

16.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.

17.

Representing a set of reconciliations in a compact way.

Scornavacca C, Paprotny W, Berry V, Ranwez V.

J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28.

PMID:
23600816
18.

A first step toward computing all hybridization networks for two rooted binary phylogenetic trees.

Scornavacca C, Linz S, Albrecht B.

J Comput Biol. 2012 Nov;19(11):1227-42. doi: 10.1089/cmb.2012.0192.

PMID:
23134319
19.

Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

Huson DH, Scornavacca C.

Syst Biol. 2012 Dec 1;61(6):1061-7. doi: 10.1093/sysbio/sys062. Epub 2012 Jul 10.

PMID:
22780991
20.

Fast computation of minimum hybridization networks.

Albrecht B, Scornavacca C, Cenci A, Huson DH.

Bioinformatics. 2012 Jan 15;28(2):191-7. doi: 10.1093/bioinformatics/btr618. Epub 2011 Nov 9.

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