Blog
About

11
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found
      Is Open Access

      Good-bye Scydmaenidae, or why the ant-like stone beetles should become megadiverse Staphylinidae sensu latissimo (Coleoptera)

      ,

      European Journal of Entomology

      Biology Centre, AS CR

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Related collections

          Most cited references 29

          • Record: found
          • Abstract: not found
          • Article: not found

          MrBayes bayesian phylogenetic inference under mixed models

            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            The Clustal X windows interfaces: flexible strategies for multiple sequence alignment aided by quality analysis tools.

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              MAFFT version 5: improvement in accuracy of multiple sequence alignment

              The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences. Like the previously available options, the new options of MAFFT can handle hundreds of sequences on a standard desktop computer. We also examined the effect of the number of homologues included in an alignment. For a multiple alignment consisting of ∼8 sequences with low similarity, the accuracy was improved (2–10 percentage points) when the sequences were aligned together with dozens of their close homologues (E-value < 10−5–10−20) collected from a database. Such improvement was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homologues collected from SwissProt using NCBI-BLAST.
                Bookmark

                Author and article information

                Journal
                European Journal of Entomology
                Eur. J. Entomol.
                EUR J ENTOMOL
                Biology Centre, AS CR
                12105759
                18028829
                May 20 2009
                May 20 2009
                : 106
                : 2
                : 275-301
                Article
                10.14411/eje.2009.035
                © 2009

                https://creativecommons.org/licenses/by/4.0/

                Product

                Comments

                Comment on this article

                Similar content 1,213

                Cited by 35

                Most referenced authors 271