Package org.episteme.natural.biology.loaders.phyloxml

package org.episteme.natural.biology.loaders.phyloxml

PhyloXML loader for phylogenetic tree data.

This package provides classes for parsing PhyloXML files containing evolutionary tree structures with taxonomy, sequence, and event annotations.

See Also:

• PhyloXML.org

Related Packages

Package	Description
org.episteme.natural.biology.loaders
org.episteme.natural.biology.loaders.biopax	BioPAX loader for biological pathways and networks.
org.episteme.natural.biology.loaders.itis	Biological taxonomy, genetics, and physiological modeling.
org.episteme.natural.biology.loaders.neuroml	NeuroML loader for computational neuroscience models.
org.episteme.natural.biology.loaders.pdbml	PDBML loader for Protein Data Bank macromolecular structures.
org.episteme.natural.biology.loaders.sbml	Systems Biology Markup Language (SBML) loader for Episteme.

Class	Description
PhyloXMLBridge	Bridge for converting PhyloXML DTOs to core Episteme evolutionary biology objects.
PhyloXMLClade	Represents a clade (node) in a PhyloXML document.
PhyloXMLDocument	Represents a parsed PhyloXML document.
PhyloXMLEvents	Represents evolutionary events in a PhyloXML document.
PhyloXMLException	Exception thrown when PhyloXML parsing fails.
PhyloXMLPhylogeny	Represents a phylogeny in a PhyloXML document.
PhyloXMLReader	PhyloXML Reader for phylogenetic tree data.
PhyloXMLSequenceInfo	Represents sequence associations in a PhyloXML document.
PhyloXMLTaxonomy	Represents taxonomic information in a PhyloXML document.