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Items: 1 to 20 of 186

1.

MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment.

Kumar S, Tamura K, Nei M.

Brief Bioinform. 2004 Jun;5(2):150-63.

PMID:
15260895
2.

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.

Tamura K, Dudley J, Nei M, Kumar S.

Mol Biol Evol. 2007 Aug;24(8):1596-9. Epub 2007 May 7.

PMID:
17488738
3.

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.

4.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

5.
6.

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.

PMID:
15647305
7.

MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers.

Kumar S, Tamura K, Nei M.

Comput Appl Biosci. 1994 Apr;10(2):189-91.

PMID:
8019868
8.

Scoredist: a simple and robust protein sequence distance estimator.

Sonnhammer EL, Hollich V.

BMC Bioinformatics. 2005 Apr 27;6:108.

9.
10.

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

11.

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W38-42. Epub 2007 Apr 22.

13.

Toward extracting all phylogenetic information from matrices of evolutionary distances.

Roch S.

Science. 2010 Mar 12;327(5971):1376-9. doi: 10.1126/science.1182300.

14.

PhyloPat: phylogenetic pattern analysis of eukaryotic genes.

Hulsen T, de Vlieg J, Groenen PM.

BMC Bioinformatics. 2006 Sep 1;7:398.

15.

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.

Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T.

Science. 2009 Jun 19;324(5934):1561-4. doi: 10.1126/science.1171243.

16.

OMA Browser--exploring orthologous relations across 352 complete genomes.

Schneider A, Dessimoz C, Gonnet GH.

Bioinformatics. 2007 Aug 15;23(16):2180-2. Epub 2007 Jun 1.

PMID:
17545180
17.

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.

Kumar S, Nei M, Dudley J, Tamura K.

Brief Bioinform. 2008 Jul;9(4):299-306. doi: 10.1093/bib/bbn017. Epub 2008 Apr 16.

18.

Computational analysis of evolution and conservation in a protein superfamily.

Irving JA, Askew DJ, Whisstock JC.

Methods. 2004 Feb;32(2):73-92.

PMID:
14698621
19.

The application of molecular phylogenetics to the analysis of viral genome diversity and evolution.

McCormack GP, Clewley JP.

Rev Med Virol. 2002 Jul-Aug;12(4):221-38. Review.

PMID:
12125014
20.

Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome.

Kosiol C, Bofkin L, Whelan S.

J Biomed Inform. 2006 Feb;39(1):51-61. Epub 2005 Sep 15. Review.

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