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Results: 1 to 20 of 118

1.

Estimating maximum likelihood phylogenies with PhyML.

Guindon S, Delsuc F, Dufayard JF, Gascuel O.

Methods Mol Biol. 2009;537:113-37. doi: 10.1007/978-1-59745-251-9_6.

PMID:
19378142
[PubMed - indexed for MEDLINE]
2.

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.

PMID:
15980534
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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
[PubMed - indexed for MEDLINE]
4.

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

Guindon S, Gascuel O.

Syst Biol. 2003 Oct;52(5):696-704.

PMID:
14530136
[PubMed - indexed for MEDLINE]
5.

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
[PubMed - indexed for MEDLINE]
Free Article
6.

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.

Gouy M, Guindon S, Gascuel O.

Mol Biol Evol. 2010 Feb;27(2):221-4. doi: 10.1093/molbev/msp259. Epub 2009 Oct 23.

PMID:
19854763
[PubMed - indexed for MEDLINE]
Free Article
7.

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
[PubMed - indexed for MEDLINE]
Free Article
8.

PALM: a paralleled and integrated framework for phylogenetic inference with automatic likelihood model selectors.

Chen SH, Su SY, Lo CZ, Chen KH, Huang TJ, Kuo BH, Lin CY.

PLoS One. 2009 Dec 7;4(12):e8116. doi: 10.1371/journal.pone.0008116.

PMID:
19997614
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis.

Wang HC, Susko E, Roger AJ.

BMC Evol Biol. 2009 Sep 8;9:225. doi: 10.1186/1471-2148-9-225.

PMID:
19737395
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.

Helaers R, Milinkovitch MC.

BMC Bioinformatics. 2010 Jul 15;11:379. doi: 10.1186/1471-2105-11-379.

PMID:
20633263
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

PMID:
15921531
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

EPoS: a modular software framework for phylogenetic analysis.

Griebel T, Brinkmeyer M, Böcker S.

Bioinformatics. 2008 Oct 15;24(20):2399-400. doi: 10.1093/bioinformatics/btn364. Epub 2008 Jul 16.

PMID:
18632748
[PubMed - indexed for MEDLINE]
Free Article
13.

FastTree 2--approximately maximum-likelihood trees for large alignments.

Price MN, Dehal PS, Arkin AP.

PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490.

PMID:
20224823
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

Dang CC, Lefort V, Le VS, Le QS, Gascuel O.

Bioinformatics. 2011 Oct 1;27(19):2758-60. doi: 10.1093/bioinformatics/btr435. Epub 2011 Jul 26.

PMID:
21791535
[PubMed - indexed for MEDLINE]
Free Article
15.

Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.

Le SQ, Gascuel O.

Syst Biol. 2010 May;59(3):277-87. doi: 10.1093/sysbio/syq002. Epub 2010 Mar 10.

PMID:
20525635
[PubMed - indexed for MEDLINE]
16.

morePhyML: improving the phylogenetic tree space exploration with PhyML 3.

Criscuolo A.

Mol Phylogenet Evol. 2011 Dec;61(3):944-8. doi: 10.1016/j.ympev.2011.08.029. Epub 2011 Sep 8.

PMID:
21925283
[PubMed - indexed for MEDLINE]
17.

A structural EM algorithm for phylogenetic inference.

Friedman N, Ninio M, Pe'er I, Pupko T.

J Comput Biol. 2002;9(2):331-53.

PMID:
12015885
[PubMed - indexed for MEDLINE]
18.

Efficient likelihood computations with nonreversible models of evolution.

Boussau B, Gouy M.

Syst Biol. 2006 Oct;55(5):756-68.

PMID:
17060197
[PubMed - indexed for MEDLINE]
19.

PAML 4: phylogenetic analysis by maximum likelihood.

Yang Z.

Mol Biol Evol. 2007 Aug;24(8):1586-91. Epub 2007 May 4.

PMID:
17483113
[PubMed - indexed for MEDLINE]
Free Article
20.

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
[PubMed - indexed for MEDLINE]

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