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bold: The Barcode of Life Data System ( http://www.barcodinglife.org)

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      Abstract

      The Barcode of Life Data System ( bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

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      Most cited references 30

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        The neighbor-joining method: a new method for reconstructing phylogenetic trees.

         N Saitou,  M Nei (1987)
        A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
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          Base-calling of automated sequencer traces using phred. II. Error probabilities.

           B T Ewing,  P. Green (1998)
          Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing program consed.
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            Author and article information

            Affiliations
            simpleCanadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph Guelph, ON, Canada N1G 2W1
            Author notes
            Correspondence: Paul Hebert, Fax: 519-767-1656. E-mail: phebert@ 123456uoguelph.ca
            Journal
            Mol Ecol Notes
            men
            Molecular Ecology Notes
            Blackwell Publishing Ltd
            1471-8278
            1471-8286
            01 May 2007
            : 7
            : 3
            : 355-364
            1890991
            18784790
            10.1111/j.1471-8286.2007.01678.x
            © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd
            Categories
            Barcodings

            Ecology

            coi, gene sequence, species identification, informatics, dna barcoding, taxonomy

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