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Items: 1 to 20 of 79

1.

Faster exact maximum parsimony search with XMP.

White WT, Holland BR.

Bioinformatics. 2011 May 15;27(10):1359-67. doi: 10.1093/bioinformatics/btr147. Epub 2011 Mar 27.

PMID:
21444294
2.

Ancestral maximum likelihood of evolutionary trees is hard.

Addario-Berry L, Chor B, Hallett M, Lagergren J, Panconesi A, Wareham T.

J Bioinform Comput Biol. 2004 Jun;2(2):257-71.

PMID:
15297981
3.
4.

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.

PMID:
16234323
5.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.

Stamatakis A, Ludwig T, Meier H.

Bioinformatics. 2005 Feb 15;21(4):456-63. Epub 2004 Dec 17.

PMID:
15608047
6.
7.

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous.

Kolaczkowski B, Thornton JW.

Nature. 2004 Oct 21;431(7011):980-4.

PMID:
15496922
9.

Parsimony accelerated maximum likelihood searches.

Sundberg K, O'Connor T, Carroll H, Clement M, Snell Q.

Int J Comput Biol Drug Des. 2008;1(1):74-87.

PMID:
20055002
10.

Towards improving searches for optimal phylogenies.

Ford E, St John K, Wheeler WC.

Syst Biol. 2015 Jan;64(1):56-65. doi: 10.1093/sysbio/syu065. Epub 2014 Aug 26.

PMID:
25164916
12.

Estimating trees from filtered data: identifiability of models for morphological phylogenetics.

Allman ES, Holder MT, Rhodes JA.

J Theor Biol. 2010 Mar 7;263(1):108-19. doi: 10.1016/j.jtbi.2009.12.001. Epub 2009 Dec 11.

PMID:
20004210
13.

Molecular phylogeny of the carnivora (mammalia): assessing the impact of increased sampling on resolving enigmatic relationships.

Flynn JJ, Finarelli JA, Zehr S, Hsu J, Nedbal MA.

Syst Biol. 2005 Apr;54(2):317-37.

PMID:
16012099
14.
15.

Characterizing the phylogenetic tree-search problem.

Money D, Whelan S.

Syst Biol. 2012 Mar;61(2):228-39. doi: 10.1093/sysbio/syr097. Epub 2011 Nov 10.

PMID:
22076302
16.

rely.py, a python script to detect reliable clades.

Li B, Dettai A, Lecointre G.

Mol Phylogenet Evol. 2010 Jan;54(1):306-8. doi: 10.1016/j.ympev.2009.09.034. Epub 2009 Oct 2.

PMID:
19800976
17.

Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data.

Wright AM, Hillis DM.

PLoS One. 2014 Oct 3;9(10):e109210. doi: 10.1371/journal.pone.0109210. eCollection 2014.

18.

Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins.

Hill T, Lundgren A, Fredriksson R, Schiöth HB.

Biochim Biophys Acta. 2005 Aug 30;1725(1):19-29.

PMID:
15990235
19.
20.

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees.

Izquierdo-Carrasco F, Smith SA, Stamatakis A.

BMC Bioinformatics. 2011 Dec 13;12:470. doi: 10.1186/1471-2105-12-470.

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