Bioinformatics Vol. 16 no. 2 2000
Pages 101-103
© 2000 Oxford University Press
Darwin v. 2.0: an interpreted computer language for the biosciences
1 Department of Computer Science, ETH Zürich, Zürich, Switzerland
To whom correspondence should be addressed.
Motivation: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems.
Results: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs.
Availability: Darwin is made available for most operating systems free of charge from the Computational Biochemistry Research Group (CBRG), reachable at http://cbrg.inf.ethz.ch.
Contact: darwin{at}inf.ethz.ch
Received on June 16, 1999
; revised on August 31, 1999
; accepted on September 14, 1999
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. T. Konstantinidis, M. H. Serres, M. F. Romine, J. L. M. Rodrigues, J. Auchtung, L.-A. McCue, M. S. Lipton, A. Obraztsova, C. S. Giometti, K. H. Nealson, et al. Comparative systems biology across an evolutionary gradient within the Shewanella genus PNAS, September 15, 2009; 106(37): 15909 - 15914. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. A. Nahum, S. Goswami, and M. H. Serres Protein families reflect the metabolic diversity of organisms and provide support for functional prediction Physiol Genomics, August 7, 2009; 38(3): 250 - 260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Schneider, A. Souvorov, N. Sabath, G. Landan, G. H. Gonnet, and D. Graur Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment Gen Biol Evol, June 22, 2009; 2009(0): 114 - 118. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Schneider and G. M. Cannarozzi Support Patterns from Different Outgroups Provide a Strong Phylogenetic Signal Mol. Biol. Evol., June 1, 2009; 26(6): 1259 - 1272. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Anisimova and C. Kosiol Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models Mol. Biol. Evol., February 1, 2009; 26(2): 255 - 271. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T Holder, D. J Zwickl, and C. Dessimoz Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes Phil Trans R Soc B, December 27, 2008; 363(1512): 4013 - 4021. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Lemoine, B. Labedan, and C. Froidevaux GenoQuery: a new querying module for functional annotation in a genomic warehouse Bioinformatics, July 1, 2008; 24(13): i322 - i329. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. C. Fulton, M. Stettler, T. Mettler, C. K. Vaughan, J. Li, P. Francisco, M. Gil, H. Reinhold, S. Eicke, G. Messerli, et al. {beta}-AMYLASE4, a Noncatalytic Protein Required for Starch Breakdown, Acts Upstream of Three Active {beta}-Amylases in Arabidopsis Chloroplasts PLANT CELL, April 1, 2008; 20(4): 1040 - 1058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Schneider, C. Dessimoz, and G. H. Gonnet OMA Browser Exploring orthologous relations across 352 complete genomes Bioinformatics, August 15, 2007; 23(16): 2180 - 2182. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. R. Johnston, C. O'Dushlaine, D. A. Fitzpatrick, R. J. Edwards, and D. C. Shields Evaluation of Whether Accelerated Protein Evolution in Chordates Has Occurred before, after, or Simultaneously with Gene Duplication Mol. Biol. Evol., January 1, 2007; 24(1): 315 - 323. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Dessimoz, B. Boeckmann, A. C. J. Roth, and G. H. Gonnet Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits Nucleic Acids Res., July 11, 2006; 34(11): 3309 - 3316. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. H. Serres and M. Riley Genomic Analysis of Carbon Source Metabolism of Shewanella oneidensis MR-1: Predictions versus Experiments J. Bacteriol., July 1, 2006; 188(13): 4601 - 4609. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Rudolph, G. Semini, F. Hauser, A. Lindemann, M. Friberg, H. Hennecke, and H.-M. Fischer The Iron Control Element, Acting in Positive and Negative Control of Iron-Regulated Bradyrhizobium japonicum Genes, Is a Target for the Irr Protein J. Bacteriol., January 15, 2006; 188(2): 733 - 744. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Massar, M. Travers, J. Elhai, and J. Shrager BioLingua: a programmable knowledge environment for biologists Bioinformatics, January 15, 2005; 21(2): 199 - 207. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Roth, M. J. Betts, P. Steffansson, G. Saelensminde, and D. A. Liberles The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D495 - D497. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Sinha, P. R. Langford, and J. S. Kroll Functional diversity of three different DsbA proteins from Neisseria meningitidis Microbiology, September 1, 2004; 150(9): 2993 - 3000. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. H. Serres, S. Goswami, and M. Riley GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins Nucleic Acids Res., January 1, 2004; 32(90001): D300 - 302. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Liang, B. Labedan, and M. Riley Physiological genomics of Escherichia coli protein families Physiol Genomics, April 10, 2002; 9(1): 15 - 26. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Liang, B. Labedan, and M. Riley Physiological genomics of Escherichia coli protein families Physiol Genomics, April 10, 2002; 9(1): 15 - 26. [Abstract] [Full Text] [PDF]
|
|