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Items: 1 to 20 of 121

1.

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.

Marcet-Houben M, Gabaldón T.

Nucleic Acids Res. 2011 May;39(10):e66. doi: 10.1093/nar/gkr087. Epub 2011 Feb 18.

2.

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.

Chaudhary R, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S11. doi: 10.1186/1471-2105-13-S10-S11.

3.

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

Górecki P, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S14. doi: 10.1186/1471-2105-13-S10-S14.

4.

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

Górecki P, Burleigh GJ, Eulenstein O.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S15. doi: 10.1186/1471-2105-12-S1-S15.

5.

iGTP: a software package for large-scale gene tree parsimony analysis.

Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O.

BMC Bioinformatics. 2010 Nov 23;11:574. doi: 10.1186/1471-2105-11-574.

6.

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA.

J Mol Evol. 2006 Aug;63(2):240-50. Epub 2006 Jul 7.

PMID:
16830091
7.

Phylogenetic identification of lateral genetic transfer events.

Beiko RG, Hamilton N.

BMC Evol Biol. 2006 Feb 11;6:15.

8.

A simple algorithm to infer gene duplication and speciation events on a gene tree.

Zmasek CM, Eddy SR.

Bioinformatics. 2001 Sep;17(9):821-8.

PMID:
11590098
9.

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.

Bansal MS, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S42. doi: 10.1186/1471-2105-11-S1-S42.

10.

Algorithms for genome-scale phylogenetics using gene tree parsimony.

Bansal MS, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):939-56. doi: 10.1109/TCBB.2013.103.

PMID:
24334388
11.

Reconciliation with non-binary species trees.

Vernot B, Stolzer M, Goldman A, Durand D.

J Comput Biol. 2008 Oct;15(8):981-1006. doi: 10.1089/cmb.2008.0092.

12.

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae.

Ness RW, Graham SW, Barrett SC.

Mol Biol Evol. 2011 Nov;28(11):3009-18. doi: 10.1093/molbev/msr119. Epub 2011 Jun 1.

PMID:
21633114
13.

Models, algorithms and programs for phylogeny reconciliation.

Doyon JP, Ranwez V, Daubin V, Berry V.

Brief Bioinform. 2011 Sep;12(5):392-400. doi: 10.1093/bib/bbr045. Review.

PMID:
21949266
15.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
16.

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss.

Bansal MS, Alm EJ, Kellis M.

Bioinformatics. 2012 Jun 15;28(12):i283-91. doi: 10.1093/bioinformatics/bts225.

17.
18.

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G.

Bioinformatics. 2005 Jun 1;21(11):2596-603. Epub 2005 Feb 15.

PMID:
15713731
19.

Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.

Burleigh JG, Bansal MS, Wehe A, Eulenstein O.

J Comput Biol. 2009 Aug;16(8):1071-83. doi: 10.1089/cmb.2009.0139.

PMID:
19689214
20.

Genome-wide probabilistic reconciliation analysis across vertebrates.

Mahmudi O, Sjöstrand J, Sennblad B, Lagergren J.

BMC Bioinformatics. 2013;14 Suppl 15:S10. doi: 10.1186/1471-2105-14-S15-S10. Epub 2013 Oct 15.

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