bioperl

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.

Keywords for this software

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References in zbMATH (referenced in 20 articles )

Showing results 1 to 20 of 20.
Sorted by year (citations)

  1. Wicke, Kristina; Fischer, Mareike: Phylogenetic diversity and biodiversity indices on phylogenetic networks (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Wicke, Kristina; Fischer, Mareike: Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value (2017)
  4. Berk Ekmekci, Charles E. McAnany, Cameron Mura: An Introduction to Programming for Bioscientists: A Python-based Primer (2016) arXiv
  5. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  6. Singh, Gautam B.: Fundamentals of bioinformatics and computational biology. Methods and exercises in MATLAB (2015)
  7. Giraud, Mathieu; Varré, Jean-Stéphane: Parallel position weight matrices algorithms (2011) ioport
  8. Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni: ETE: a python environment for tree exploration (2010) ioport
  9. Merelo Guervós, Juan Julián; Castillo, Pedro A.; Alba, Enrique: Algorithm::Evolutionary, a flexible Perl module for evolutionary computation (2010) ioport
  10. Han, Mira V.; Zmasek, Christian M.: Phyloxml: XML for evolutionary biology and comparative genomics (2009) ioport
  11. 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
  12. Papanicolaou, Alexie; Stierli, Remo; Ffrench-Constant, Richard H.; Heckel, David G.: Next generation transcriptomes for next generation genomes using \textitest2assembly (2009) ioport
  13. Schreiber, Fabian; Pick, Kerstin; Erpenbeck, Dirk; Wörheide, Gert; Morgenstern, Burkhard: Orthoselect: a protocol for selecting orthologous groups in phylogenomics (2009) ioport
  14. Doring, Andreas; Weese, David; Rausch, Tobias; Reinert, Knut: Seqan - an efficient, generic C++ library for sequence analysis (2008) ioport
  15. Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente: A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks (2008) arXiv
  16. Sipos, Botond; Somogyi, Kalman; Ando, Istvan; Penzes, Zsolt: T2prhd: a tool to study the patterns of repeat evolution (2008) ioport
  17. 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
  18. Jithesh, P. V.; Donachy, P.; Harmer, T.; Kelly, N.; Perrott, R.; Wasnik, S.; Johnston, J.; McCurley, M.; Townsley, M.; McKee, S.: GeneGrid: Architecture, implementation and application (2006)
  19. Jithesh, P. V.; Donachy, P.; Harmer, T.; Kelly, N.; Perrott, R.; Wasnik, S.; Johnston, J.; McCurley, M.; Townsley, M.; McKee, S.: GeneGrid: Architecture, implementation and application (2006) ioport
  20. Llabrés, Mercè; Rocha, Jairo; Rosselló, Francesc; Valiente, Gabriel: On the ancestral compatibility of two phylogenetic trees with nested taxa (2006)