The bioperl toolkit: Perl modules for the life sciences. BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository.

References in zbMATH (referenced in 23 articles )

Showing results 1 to 20 of 23.
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  1. Bouckaert, Remco; Fischer, Mareike; Wicke, Kristina: Combinatorial perspectives on Dollo-(k) characters in phylogenetics (2021)
  2. Wicke, Kristina; Fischer, Mareike: Phylogenetic diversity and biodiversity indices on phylogenetic networks (2018)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Wicke, Kristina; Fischer, Mareike: Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value (2017)
  5. Berk Ekmekci, Charles E. McAnany, Cameron Mura: An Introduction to Programming for Bioscientists: A Python-based Primer (2016) arXiv
  6. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  7. Singh, Gautam B.: Fundamentals of bioinformatics and computational biology. Methods and exercises in MATLAB (2015)
  8. Lafond, Manuel; Swenson, Krister M.; El-Mabrouk, Nadia: Error detection and correction of gene trees (2013)
  9. Giraud, Mathieu; Varré, Jean-Stéphane: Parallel position weight matrices algorithms (2011) ioport
  10. Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni: ETE: a python environment for tree exploration (2010) ioport
  11. Merelo Guervós, Juan Julián; Castillo, Pedro A.; Alba, Enrique: Algorithm::Evolutionary, a flexible Perl module for evolutionary computation (2010) ioport
  12. Han, Mira V.; Zmasek, Christian M.: Phyloxml: XML for evolutionary biology and comparative genomics (2009) ioport
  13. Liang, Chunguang; Schmid, Alexander; López-Sánchez, María José; Moya, Andres; Gross, Roy; Bernhardt, Jörg; Dandekar, Thomas: JANE: efficient mapping of prokaryotic ests and variable length sequence reads on related template genomes (2009) ioport
  14. Papanicolaou, Alexie; Stierli, Remo; Ffrench-Constant, Richard H.; Heckel, David G.: Next generation transcriptomes for next generation genomes using \textitest2assembly (2009) ioport
  15. Schreiber, Fabian; Pick, Kerstin; Erpenbeck, Dirk; Wörheide, Gert; Morgenstern, Burkhard: Orthoselect: a protocol for selecting orthologous groups in phylogenomics (2009) ioport
  16. Valiente, Gabriel: Combinatorial pattern matching algorithms in computational biology using Perl and R. (2009)
  17. Doring, Andreas; Weese, David; Rausch, Tobias; Reinert, Knut: Seqan - an efficient, generic C++ library for sequence analysis (2008) ioport
  18. Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente: A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks (2008) arXiv
  19. Sipos, Botond; Somogyi, Kalman; Ando, Istvan; Penzes, Zsolt: T2prhd: a tool to study the patterns of repeat evolution (2008) ioport
  20. Givan, Scott A.; Sullivan, Christopher M.; Carrington, James C.: The personal sequence database: a suite of tools to create and maintain web-accessible sequence databases (2007) ioport

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