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Items: 1 to 20 of 114

1.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.

2.

Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.

BMC Bioinformatics. 2006 Apr 4;7:188.

3.

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.

Dutheil J, Boussau B.

BMC Evol Biol. 2008 Sep 22;8:255. doi: 10.1186/1471-2148-8-255.

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BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.

7.

MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.

Cai JJ, Smith DK, Xia X, Yuen KY.

BMC Bioinformatics. 2005 Mar 22;6:64.

8.

MafFilter: a highly flexible and extensible multiple genome alignment files processor.

Dutheil JY, Gaillard S, Stukenbrock EH.

BMC Genomics. 2014 Jan 22;15:53. doi: 10.1186/1471-2164-15-53.

9.

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience.

Corradi L, Porro I, Schenone A, Momeni P, Ferrari R, Nobili F, Ferrara M, Arnulfo G, Fato MM.

BMC Med Inform Decis Mak. 2012 Oct 8;12:115. doi: 10.1186/1472-6947-12-115.

10.

A library of efficient bioinformatics algorithms.

Della Vedova G, Dondi R.

Appl Bioinformatics. 2003;2(2):117-21. Review.

PMID:
15130828
11.

MultiSeq: unifying sequence and structure data for evolutionary analysis.

Roberts E, Eargle J, Wright D, Luthey-Schulten Z.

BMC Bioinformatics. 2006 Aug 16;7:382.

12.

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

Drummond A, Strimmer K.

Bioinformatics. 2001 Jul;17(7):662-3.

13.

The Bioinformatics Template Library--generic components for biocomputing.

Pitt WR, Williams MA, Steven M, Sweeney B, Bleasby AJ, Moss DS.

Bioinformatics. 2001 Aug;17(8):729-37.

14.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

15.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K.

PLoS One. 2007 Aug 22;2(8):e766.

16.

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.

17.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S12. doi: 10.1186/1471-2105-11-S12-S12.

18.

The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.

Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A.

J Biotechnol. 2009 Mar 10;140(1-2):3-12.

PMID:
19297685
19.

MACSIMS: multiple alignment of complete sequences information management system.

Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O.

BMC Bioinformatics. 2006 Jun 23;7:318.

20.

SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.

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