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A comparison of common programming languages used in bioinformatics.

Fourment M, Gillings MR.

BMC Bioinformatics. 2008 Feb 5;9:82.PMID: 18251993 [PubMed - indexed for MEDLINE]Related articlesFree article

Open source clustering software.

de Hoon MJ, Imoto S, Nolan J, Miyano S.

Bioinformatics. 2004 Jun 12;20(9):1453-4. Epub 2004 Feb 10.PMID: 14871861 [PubMed - indexed for MEDLINE]Related articlesFree article

Automated programming for bioinformatics algorithm deployment.

Alterovitz G, Jiwaji A, Ramoni MF.

Bioinformatics. 2008 Feb 1;24(3):450-1. Epub 2008 Jan 3.PMID: 18174185 [PubMed - indexed for MEDLINE]Related articlesFree article

LibSBML: an API library for SBML.

Bornstein BJ, Keating SM, Jouraku A, Hucka M.

Bioinformatics. 2008 Mar 15;24(6):880-1. Epub 2008 Feb 5.PMID: 18252737 [PubMed - indexed for MEDLINE]Related articlesFree article

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. Epub 2009 Mar 20.PMID: 19304878 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 11524374 [PubMed - indexed for MEDLINE]Related articlesFree article

MolTalk--a programming library for protein structures and structure analysis.

Diemand AV, Scheib H.

BMC Bioinformatics. 2004 Apr 19;5:39.PMID: 15096277 [PubMed - indexed for MEDLINE]Related articlesFree article

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. Epub 2008 Aug 8.PMID: 18689808 [PubMed - indexed for MEDLINE]Related articlesFree article

Designing and executing scientific workflows with a programmable integrator.

Chagoyen M, Kurul ME, De-Alarcón PA, Carazo JM, Gupta A.

Bioinformatics. 2004 Sep 1;20(13):2092-100. Epub 2004 Apr 1.PMID: 15059834 [PubMed - indexed for MEDLINE]Related articlesFree article

Bioclipse: an open source workbench for chemo- and bioinformatics.

Spjuth O, Helmus T, Willighagen EL, Kuhn S, Eklund M, Wagener J, Murray-Rust P, Steinbeck C, Wikberg JE.

BMC Bioinformatics. 2007 Feb 22;8:59.PMID: 17316423 [PubMed - indexed for MEDLINE]Related articlesFree article

VECT: an automatic visual Perl programming tool for nonprogrammers.

Chou HH.

Biotechniques. 2005 Apr;38(4):615-21.PMID: 15884679 [PubMed - indexed for MEDLINE]Related articlesFree article

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano MM, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31. Review.PMID: 18238804 [PubMed - indexed for MEDLINE]Related articles

A library of efficient bioinformatics algorithms.

Della Vedova G, Dondi R.

Appl Bioinformatics. 2003;2(2):117-21. Review.PMID: 15130828 [PubMed - indexed for MEDLINE]Related articles

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.PMID: 17586553 [PubMed - indexed for MEDLINE]Related articlesFree article

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

Ji X, Xu Y.

Bioinformatics. 2006 Jan 1;22(1):124-6. Epub 2005 Nov 2.PMID: 16267082 [PubMed - indexed for MEDLINE]Related articlesFree article

Clearcut: a fast implementation of relaxed neighbor joining.

Sheneman L, Evans J, Foster JA.

Bioinformatics. 2006 Nov 15;22(22):2823-4. Epub 2006 Sep 18.PMID: 16982706 [PubMed - indexed for MEDLINE]Related articlesFree article

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

Shahid M, Alam I, Fuellen G.

Appl Bioinformatics. 2006;5(1):63-6.PMID: 16539540 [PubMed - indexed for MEDLINE]Related articles

Utility library for structural bioinformatics.

Gront D, Kolinski A.

Bioinformatics. 2008 Feb 15;24(4):584-5. Epub 2008 Jan 28.PMID: 18227118 [PubMed - indexed for MEDLINE]Related articlesFree article

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.

Nye TM, Liò P, Gilks WR.

Bioinformatics. 2006 Jan 1;22(1):117-9. Epub 2005 Oct 18.PMID: 16234319 [PubMed - indexed for MEDLINE]Related articlesFree article

HotSwap for bioinformatics: a STRAP tutorial.

Gille C, Robinson PN.

BMC Bioinformatics. 2006 Feb 9;7:64.PMID: 16469097 [PubMed - indexed for MEDLINE]Related articlesFree article