| This Release | Bio-Phylo-0.17_RC6 | [Download] [Browse] | 20 Jul 2007 | |||
| Latest Release | Bio-Phylo-0.17_RC9 | [Download] [Browse] | 04 Mar 2009 | |||
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| Links | [ Discussion Forum ] [ View/Report Bugs (1) ] [ Dependencies ] [ Other Tools ] | |||||
| CPAN Testers | PASS (101) FAIL (17) [ View Reports ] [ Perl/Platform Version Matrix ] | |||||
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| License | Unknown | |||||
| Special Files |
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| Bio::Phylo | Phylogenetic analysis using perl. | 0.17_RC6 | |
| Bio::Phylo::Adaptor | Object adaptor for compatibility | ||
| Bio::Phylo::Adaptor::Bioperl::Datum | Adaptor class for bioperl compatibility | ||
| Bio::Phylo::Adaptor::Bioperl::Matrix | Adaptor class for bioperl compatibility | ||
| Bio::Phylo::Adaptor::Bioperl::Node | Adaptor class for bioperl compatibility | ||
| Bio::Phylo::Adaptor::Bioperl::Tree | Adaptor class for bioperl compatibility | ||
| Bio::Phylo::Forest | The forest object, a set of phylogenetic trees. | ||
| Bio::Phylo::Forest::Node | The tree node object. | ||
| Bio::Phylo::Forest::Tree | The tree object. | ||
| Bio::Phylo::Generator | Generates random trees. | ||
| Bio::Phylo::IO | Input and output of phylogenetic data. | ||
| Bio::Phylo::Listable | Parent class for listable/iterator objects. | ||
| Bio::Phylo::Matrices | Holds a set of matrix objects. | ||
| Bio::Phylo::Matrices::Datatype | Superclass for objects that validate character data. | ||
| Bio::Phylo::Matrices::Datatype::Continuous | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Custom | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Dna | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Mixed | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Protein | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Restriction | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Rna | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datatype::Standard | Datatype subclass, no serviceable parts inside | ||
| Bio::Phylo::Matrices::Datum | The character state sequence object. | ||
| Bio::Phylo::Matrices::Matrix | Character state matrix. | ||
| Bio::Phylo::Matrices::TypeSafeData | Superclass for objects that hold character data. | ||
| Bio::Phylo::Mediators::NodeMediator | Mediator class to manage links between nodes. | ||
| Bio::Phylo::Mediators::TaxaMediator | Mediator class to manage links between objects. | ||
| Bio::Phylo::Parsers::Newick | Parses newick trees. No serviceable parts inside. | ||
| Bio::Phylo::Parsers::Nexus | Parses nexus files. No serviceable parts inside. | ||
| Bio::Phylo::Parsers::Table | Parses tab- (or otherwise) delimited matrices. No serviceable parts inside. | ||
| Bio::Phylo::Parsers::Taxlist | Parses lists of taxon names. No serviceable parts inside. | ||
| Bio::Phylo::Taxa | An object-oriented module for managing taxa. | ||
| Bio::Phylo::Taxa::TaxaLinker | Superclass for objects that link to taxa objects. | ||
| Bio::Phylo::Taxa::Taxon | The operational taxonomic unit. | ||
| Bio::Phylo::Taxa::TaxonLinker | Superclass for objects that link to taxon objects. | ||
| Bio::Phylo::Treedrawer | An object-oriented facade for drawing trees. | ||
| Bio::Phylo::Treedrawer::Svg | Creates svg tree drawings. No serviceable parts inside. | ||
| Bio::Phylo::Unparsers::Mrp | Unparses a forest object into an MRP matrix. No serviceable parts inside. | ||
| Bio::Phylo::Unparsers::Newick | Unparses newick trees. No serviceable parts inside. | ||
| Bio::Phylo::Unparsers::Nexus | Unparses nexus matrices. No serviceable parts inside. | ||
| Bio::Phylo::Unparsers::Pagel | Unparses pagel data files. No serviceable parts inside. | ||
| Bio::Phylo::Util::CONSTANT | This package defines global constants and utility functions that operate on them. | ||
| Bio::Phylo::Util::Exceptions | Exception classes for Bio::Phylo. | ||
| Bio::Phylo::Util::IDPool | Utility class for generating object IDs. No serviceable parts inside. | ||
| Bio::Phylo::Util::Logger | Logging for Bio::Phylo. | ||
| Bio::Phylo::Util::XMLWritable | Superclass for objects that stringify to xml |
| Bio::ObjectCompat | Object compatibility for phylogenetic software in OO perl |
| Bio::Phylo::Manual | Bio::Phylo user guide. |
| age2bl.pl | converts node ages to branch lengths. |
| bremer.pl | creates paup commands to calculate bremer values using parsimony ratchet. |
| dnd2svg.pl | draws newick trees as svg drawings. |
| dndtag.pl | applies unique node labels to newick trees. |
| droptip.pl | prunes a list of tips from input tree. |
