Package Bio :: Package Phylo :: Module PhyloXML
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Module PhyloXML

source code

Classes corresponding to phyloXML elements.

See Also

Official specification:
http://phyloxml.org/
Journal article:
Han and Zmasek (2009), doi:10.1186/1471-2105-10-356
Classes [hide private]
  PhyloXMLWarning
Warning for non-compliance with the phyloXML specification.
  PhyloElement
Base class for all PhyloXML objects.
  Phyloxml
Root node of the PhyloXML document.
  Other
Container for non-phyloXML elements in the tree.
  Phylogeny
A phylogenetic tree.
  Clade
Describes a branch of the current phylogenetic tree.
  BranchColor
  Accession
Captures the local part in a sequence identifier.
  Annotation
The annotation of a molecular sequence.
  BinaryCharacters
The names and/or counts of binary characters present, gained, and lost at the root of a clade.
  CladeRelation
Expresses a typed relationship between two clades.
  Confidence
A general purpose confidence element.
  Date
A date associated with a clade/node.
  Distribution
Geographic distribution of the items of a clade (species, sequences).
  DomainArchitecture
Domain architecture of a protein.
  Events
Events at the root node of a clade (e.g. one gene duplication).
  Id
A general-purpose identifier element.
  MolSeq
Store a molecular sequence.
  Point
Geographic coordinates of a point, with an optional altitude.
  Polygon
A polygon defined by a list of 'Points' (used by element 'Distribution').
  Property
A typed and referenced property from an external resources.
  ProteinDomain
Represents an individual domain in a domain architecture.
  Reference
Literature reference for a clade.
  Sequence
A molecular sequence (Protein, DNA, RNA) associated with a node.
  SequenceRelation
Express a typed relationship between two sequences.
  Taxonomy
Describe taxonomic information for a clade.
  Uri
A uniform resource identifier.
Functions [hide private]
 
_check_str(text, testfunc)
Check a string using testfunc, and warn if there's no match.
source code
Variables [hide private]
  __package__ = 'Bio.Phylo'