| This Release | Bio-NEXUS-0.69b | [Download] [Browse] | 23 Apr 2008 | |||
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| CPAN Testers | PASS (54) FAIL (78) UNKNOWN (1) [ View Reports ] [ Perl/Platform Version Matrix ] | |||||
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| License | Unknown | |||||
| Special Files |
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| Bio::NEXUS | An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format | 0.69 | |
| Bio::NEXUS::AssumptionsBlock | Represents ASSUMPTIONS block of a NEXUS file | ||
| Bio::NEXUS::Block | Provides useful functions for blocks in NEXUS file (parent class). | ||
| Bio::NEXUS::CharactersBlock | Represents a CHARACTERS Block (Data or Characters) of a NEXUS file | ||
| Bio::NEXUS::CodonsBlock | Represents CODONS block in NEXUS file | ||
| Bio::NEXUS::DataBlock | Represents the deprecated DATA Block in NEXUS file. | ||
| Bio::NEXUS::DistancesBlock | Represents DISTANCES block in NEXUS file | ||
| Bio::NEXUS::Functions | Provides private utiliy functions for the module | ||
| Bio::NEXUS::HistoryBlock | Represents a HISTORY block of a NEXUS file | ||
| Bio::NEXUS::Matrix | Provides functions for handling blocks that have matrices | ||
| Bio::NEXUS::NHXCmd | Provides functions for manipulating nodes in trees | ||
| Bio::NEXUS::Node | Provides functions for manipulating nodes in trees | ||
| Bio::NEXUS::NotesBlock | Represents a NOTES block in a NEXUS file. | ||
| Bio::NEXUS::SetsBlock | Represents SETS block of a NEXUS file | ||
| Bio::NEXUS::SpanBlock | Represent SPAN block in a NEXUS file (contains meta data). | ||
| Bio::NEXUS::TaxUnit | Represents a taxon unit in a NEXUS file | ||
| Bio::NEXUS::TaxUnitSet | Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file | ||
| Bio::NEXUS::TaxaBlock | Represents TAXA block of a NEXUS file | ||
| Bio::NEXUS::Tree | Provides functions for manipulating trees | ||
| Bio::NEXUS::TreesBlock | Represents TREES block of a NEXUS file | ||
| Bio::NEXUS::UnalignedBlock | Represents an UNALIGNED block of a NEXUS file | ||
| Bio::NEXUS::UnknownBlock | Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module. | ||
| Bio::NEXUS::Util::Exceptions | Exception classes for Bio::NEXUS. | ||
| Bio::NEXUS::Util::Logger | Logging for Bio::NEXUS. | ||
| Bio::NEXUS::WeightSet | Represents column weights in alignment ( for each character) |
| Bugs | Report for the NEXPL library |
| Changes.txt | : Contains the changes and updates made to the NEXPL library |
| Installation | Bio::NEXUS Installation Instructions. |
| Tutorial | Hands-on tutorial for using Bio::NEXUS module. |
| align2nex.pl | translate an alignment into NEXUS format using BioPerl |
| history.pl | |
| nex2text_tree.pl | Trees as strings |
| nexplot.pl | PostScript plot of tree + data table (from NEXUS infile) |
| nextool.pl | Command-line NEXUS file manipulation tool |
| p3treeplot.pl | uses R to create PPP trees from a NEXUS file |
| pppplot.pl | generates posterior probability of presence plots (SPAN) |
| this.pl | do something very important. |
| tree2nex.pl | translate a tree in DND or phylip format into NEXUS TREES block |
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README_admin |
doc/NEXUS_coverage.html |
