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  • ...informatics hackathon was (and is on a continuing basis) on leveraging the Bio* open source software tools to provide the "glue" and lower the barriers fo
    16 KB (2,281 words) - 14:01, 13 April 2016
  • ...lin) raised the issue that BioPerl has many holes in it, i.e., it defines "Bio::Run" interfaces to various
    4 KB (664 words) - 11:09, 5 September 2007
  • ...of the actual associated Tree object); this is a reference to the ongoing "Bio::CDAT" project ...ured and indexable storage than raw Nexus files would permit extending the Bio::*IO subsystems to target Nexus and/or relational schema(s)
    11 KB (1,762 words) - 11:45, 5 September 2007
  • ...ttp://www.bioperl.org/wiki/PopGen_modules Bio::PopGen], Bio::Variation and Bio::Pedigree::Marker::variation.
    34 KB (4,831 words) - 16:08, 8 November 2011
  • ...plete the support of phylogenetic and evolutionary analysis programs in '''Bio::Tools::Run''' ...this goal. Add object-relational mapping for Bioperl Bio::Tree::TreeI and Bio::Tree::NodeI objects to Bioperl-db.
    2 KB (311 words) - 11:15, 26 September 2006
  • ...re that the phyloinformatic community can contribute to (e.g. Mesquite, R, Bio* toolkits) or by advocating object and data models that the community can a The widely-used Bio* toolkits ([http://bioperl.org BioPerl], [http://biojava.org BioJava], [htt
    5 KB (605 words) - 17:20, 17 September 2013
  • A Bio::CDAT object is a composite "container" data object consisting of # one or more Bio::CDAT::TaxonSetI objects (which are containers/iterators of Bio::CDAT::TaxonI objects)
    9 KB (1,279 words) - 15:14, 3 March 2008
  • # reconcile tree problem: <br>msa + species_tree (e.g., bio::DB::Taxonomy -> njtree/phyml (or RAP) -> tree::NHX <br>BioPerl already has
    960 bytes (146 words) - 11:43, 5 September 2007
  • | Designed, implemented, and tested two new Bio::SimpleAlign (BioPerl) methods, used to protect sequence names in workflows ...ta-and-Tree (CDAT) model in BioPerl (Bio::AlignI as Bio::AnnotatableI; new Bio::Annotation::TreeI to associate tree with aligned data)
    6 KB (869 words) - 17:44, 17 September 2013
  • ...om a multitude of possible examples. The focus is on approaches that use a Bio* toolkit ([[http://www.biojava.org BioJava], [http://bioperl.org BioPerl], Based on the work of Amy Bouck (http://visionlab.bio.unc.edu/), and described in [[Media:Distr_of_Ks.pdf|her presentation]]. The
    9 KB (1,461 words) - 16:23, 3 March 2008
  • Based on the work of Stefanie Hartmann (http://visionlab.bio.unc.edu/), and described in more detail in [[Media:ReconcileTrees_Stef.pdf| #* Example: clustalw and the {{CPAN|Bio::Tools::Run::Alignment::Clustalw}} module.
    6 KB (876 words) - 16:23, 3 March 2008
  • * [http://bio.cs.washington.edu/software.html FootPrinter] ...l group has provided a new method, <code>footprint()</code>, in the {{CPAN|Bio::Tools::Run::Alignment::Clustalw}} module, found in the [http://www.bioperl
    7 KB (1,007 words) - 12:50, 5 September 2007
  • ===BioPerl and Bio::Phylo=== ...matrix objects compatible between [http://bioperl.org BioPerl] and {{CPAN|Bio::Phylo}}. BioPerl has an alignment object (i.e. a molecular matrix), but cu
    4 KB (552 words) - 16:22, 3 March 2008
  • ...:PL modules. ''Not yet done'', these modules will depend on work on {{CPAN|Bio::NEXUS}} as the input to [http://ginger.ucdavis.edu/r8s/ r8s] is a NEXUS fi
    3 KB (502 words) - 16:24, 3 March 2008
  • ...erence implementation that can be included in application software (NCL or Bio::NEXUS) ...ssembled a set of NEXUS files starting with files from the test suites for Bio::NEXUS
    41 KB (6,423 words) - 02:20, 30 March 2008
  • Two new Bio::SimpleAlign methods are written & tested: use Bio::AlignIO;
    2 KB (304 words) - 12:50, 5 September 2007
  • ==List of NEXUS keywords from the Bio::NEXUS documentation== ...ensions nchar=53;", "taxset 'beans' = 1-5,7"). Below is a table from the Bio::NEXUS documentation that lists all of the command and sub-command keywords
    19 KB (3,124 words) - 14:35, 25 March 2011
  • .../biojava/browse/biojava-live/trunk/src/org/biojavax/bio/phylo org.biojavax.bio.phylo package (SVN)] ...s.sourceforge.net/gmod/Generic-Genome-Browser/libnew/Bio/Graphics/Browser/ Bio::Graphics code within GMOD on SourceForge]
    33 KB (4,999 words) - 21:12, 22 October 2010
  • ...e standard PERL and BioPERL modules when available. These modules include: Bio::TreeIO, DBI, and Getopt::Std. The [ftp://www.treebase.org/pub/treebase/M47 **Bio::Tree:TreeI
    20 KB (2,741 words) - 16:23, 23 October 2007
  • == Appropriate bio* package: == ...is project than it appears he will now. Also, BioPerl is the most advanced Bio* toolkit and BioJava doesn't offer much functionality or object models to a
    21 KB (3,325 words) - 18:12, 23 July 2007

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