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Items: 1 to 20 of 329

1.
2.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.

Syst Biol. 2010 May;59(3):307-21. doi: 10.1093/sysbio/syq010. Epub 2010 Mar 29.

PMID:
20525638
3.

PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference.

Guindon S, Lethiec F, Duroux P, Gascuel O.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W557-9.

4.

Accelerated likelihood surface exploration: the likelihood ratchet.

Vos RA.

Syst Biol. 2003 Jun;52(3):368-73.

PMID:
12775525
5.
6.
7.

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
8.

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
9.

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
10.

SDM: a fast distance-based approach for (super) tree building in phylogenomics.

Criscuolo A, Berry V, Douzery EJ, Gascuel O.

Syst Biol. 2006 Oct;55(5):740-55.

PMID:
17060196
11.
12.

Upper bounds on maximum likelihood for phylogenetic trees.

Hendy MD, Holland BR.

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

PMID:
14534174
14.
15.

Birth-death prior on phylogeny and speed dating.

Akerborg O, Sennblad B, Lagergren J.

BMC Evol Biol. 2008 Mar 4;8:77. doi: 10.1186/1471-2148-8-77.

16.

Is multiple-sequence alignment required for accurate inference of phylogeny?

Höhl M, Ragan MA.

Syst Biol. 2007 Apr;56(2):206-21.

PMID:
17454975
18.

jModelTest: phylogenetic model averaging.

Posada D.

Mol Biol Evol. 2008 Jul;25(7):1253-6. doi: 10.1093/molbev/msn083. Epub 2008 Apr 8.

PMID:
18397919
19.

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.

Anisimova M, Gascuel O.

Syst Biol. 2006 Aug;55(4):539-52.

PMID:
16785212
20.

A rapid bootstrap algorithm for the RAxML Web servers.

Stamatakis A, Hoover P, Rougemont J.

Syst Biol. 2008 Oct;57(5):758-71. doi: 10.1080/10635150802429642.

PMID:
18853362

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