Darwin v. 2.0: an interpreted computer language for the biosciences

  title={Darwin v. 2.0: an interpreted computer language for the biosciences},
  author={G. Gonnet and M. Hallett and C. Korostensky and Laurent Bernardin},
  volume={16 2},
  • G. Gonnet, M. Hallett, +1 author Laurent Bernardin
  • Published 2000
  • Computer Science, Medicine
  • Bioinformatics
  • 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… CONTINUE READING
    113 Citations
    Investigating protein-coding sequence evolution with probabilistic codon substitution models.
    • 148
    • PDF
    ALF—A Simulation Framework for Genome Evolution
    • 123
    • PDF
    Bacterial syntenies: an exact approach with gene quorum
    • 11
    BioLingua: a programmable knowledge environment for biologists
    • 50
    • PDF
    Codon-based Models of Evolution and Applications in Mammalian Phylogeny
    • 1
    Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes
    • 48
    • PDF
    Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment
    • 113
    • PDF


    Evaluation Measures of Multiple Sequence Alignments
    • 51
    • PDF
    Near optimal multiple sequence alignments using a traveling salesman problem approach
    • C. Korostensky, G. Gonnet
    • Mathematics, Computer Science
    • 6th International Symposium on String Processing and Information Retrieval. 5th International Workshop on Groupware (Cat. No.PR00268)
    • 1999
    • 19
    The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
    • 2,043
    • PDF
    The EMBL Nucleotide Sequence Database
    • 267
    • PDF
    Probabilistic Ancestral Sequences and Multiple Alignments
    • 23
    • PDF
    The SWISS-PROT protein sequence data bank and its supplement TrEMBL
    • 1,653
    • Highly Influential
    • PDF
    The neighbor-joining method: a new method for reconstructing phylogenetic trees.
    • 50,271
    • PDF
    Algorithms on strings, trees, and sequences
    • 1,728
    • PDF
    Exhaustive matching of the entire protein sequence database.
    • 820
    • Highly Influential
    Amino acid substitution matrices from protein blocks.
    • S. Henikoff, J. Henikoff
    • Biology, Medicine
    • Proceedings of the National Academy of Sciences of the United States of America
    • 1992
    • 5,303
    • PDF