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Items: 1 to 20 of 122

1.

A consensus tree approach for reconstructing human evolutionary history and detecting population substructure.

Tsai MC, Blelloch G, Ravi R, Schwartz R.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):918-28. doi: 10.1109/TCBB.2011.23.

2.

Genome-scale coestimation of species and gene trees.

Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112. Epub 2012 Nov 6.

4.

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.

Mol Biol Evol. 2011 Oct;28(10):2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.

5.

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

6.

Properties of consensus methods for inferring species trees from gene trees.

Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA.

Syst Biol. 2009 Feb;58(1):35-54. doi: 10.1093/sysbio/syp008. Epub 2009 Jun 4.

7.

Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data.

Tsai MC, Blelloch G, Ravi R, Schwartz R.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1137-49.

8.
9.

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.

McCormack JE, Huang H, Knowles LL.

Syst Biol. 2009 Oct;58(5):501-8. doi: 10.1093/sysbio/syp045. Epub 2009 Aug 20.

PMID:
20525604
10.

Discordance of species trees with their most likely gene trees.

Degnan JH, Rosenberg NA.

PLoS Genet. 2006 May;2(5):e68. Epub 2006 May 26.

11.

Algorithms for efficient near-perfect phylogenetic tree reconstruction in theory and practice.

Sridhar S, Dhamdhere K, Blelloch G, Halperin E, Ravi R, Schwartz R.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):561-71.

PMID:
17975268
12.

Optimal algorithms for local vertex quartet cleaning.

Della Vedova G, Wareham HT.

Bioinformatics. 2002 Oct;18(10):1297-304.

PMID:
12376373
13.

Inferring phylogenetic relationships avoiding forbidden rooted triplets.

He YJ, Huynh TN, Jansson J, Sung WK.

J Bioinform Comput Biol. 2006 Feb;4(1):59-74.

PMID:
16568542
14.

Exact solutions for species tree inference from discordant gene trees.

Chang WC, Górecki P, Eulenstein O.

J Bioinform Comput Biol. 2013 Oct;11(5):1342005. doi: 10.1142/S0219720013420055. Epub 2013 Oct 2.

PMID:
24131054
15.

Consensus properties for the deep coalescence problem and their application for scalable tree search.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S12. doi: 10.1186/1471-2105-13-S10-S12.

16.

Species tree inference by minimizing deep coalescences.

Than C, Nakhleh L.

PLoS Comput Biol. 2009 Sep;5(9):e1000501. doi: 10.1371/journal.pcbi.1000501. Epub 2009 Sep 11.

17.

Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected].

Vishnoi A, Roy R, Prasad HK, Bhattacharya A.

PLoS One. 2010 Nov 30;5(11):e14159. doi: 10.1371/journal.pone.0014159. Erratum in: PLoS One. 2010;5(12) doi: 10.1371/annotation/a56d6c19-b938-4733-8333-79ff48202414.

18.

Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

Tuller T, Birin H, Kupiec M, Ruppin E.

J Comput Biol. 2010 Sep;17(9):1327-44. doi: 10.1089/cmb.2010.0112.

PMID:
20874411
19.

BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.

20.

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