Module PhyloXML

Classes corresponding to phyloXML elements.

See http://phyloxml.org/ for the official specification.

See also Han and Zmasek (2009) doi:10.1186/1471-2105-10-356

Classes

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.

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.

BranchColor
Indicates the color of a clade when rendered graphically.

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.

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

_check_str(text, testfunc)
Check a string using testfunc, and warn if there's no match.

source code

Variables

__package__ = 'Bio.Phylo'