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Items: 1 to 20 of 270

1.

IQPNNI: moving fast through tree space and stopping in time.

Vinh le S, Von Haeseler A.

Mol Biol Evol. 2004 Aug;21(8):1565-71. Epub 2004 May 26.

2.
4.

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.

5.
6.

Representation in stochastic search for phylogenetic tree reconstruction.

Weber G, Ohno-Machado L, Shieber S.

J Biomed Inform. 2006 Feb;39(1):43-50. Epub 2005 Nov 28.

8.

Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny.

Katoh K, Kuma K, Miyata T.

J Mol Evol. 2001 Oct-Nov;53(4-5):477-84.

PMID:
11675608
9.

TrExML: a maximum-likelihood approach for extensive tree-space exploration.

Wolf MJ, Easteal S, Kahn M, McKay BD, Jermiin LS.

Bioinformatics. 2000 Apr;16(4):383-94.

10.
11.

Upper bounds on maximum likelihood for phylogenetic trees.

Hendy MD, Holland BR.

Bioinformatics. 2003 Oct;19 Suppl 2:ii66-72.

12.

What if I don't have a tree? Split decomposition and related models.

Huson DH.

Curr Protoc Bioinformatics. 2003 May;Chapter 6:Unit 6.7. doi: 10.1002/0471250953.bi0607s01.

PMID:
18428706
13.

Maximum-likelihood analysis using TREE-PUZZLE.

Schmidt HA, von Haeseler A.

Curr Protoc Bioinformatics. 2007 Mar;Chapter 6:Unit 6.6. doi: 10.1002/0471250953.bi0606s17.

PMID:
18428792
14.
15.

Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

Evans J, Sheneman L, Foster J.

J Mol Evol. 2006 Jun;62(6):785-92. Epub 2006 Apr 28.

PMID:
16752216
16.

Progressive tree neighborhood applied to the maximum parsimony problem.

Goƫffon A, Richer JM, Hao JK.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):136-45. doi: 10.1109/TCBB.2007.1065.

PMID:
18245882
17.

Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood.

Hordijk W, Gascuel O.

Bioinformatics. 2005 Dec 15;21(24):4338-47. Epub 2005 Oct 18.

18.
19.

The prevalence of multifurcations in tree-space and their implications for tree-search.

Whelan S, Money D.

Mol Biol Evol. 2010 Dec;27(12):2674-7. doi: 10.1093/molbev/msq163. Epub 2010 Jun 28.

20.

Topological rearrangements and local search method for tandem duplication trees.

Bertrand D, Gascuel O.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Jan-Mar;2(1):15-28.

PMID:
17044161
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