phy:Clade

Element Clade is used in a recursive manner to describe the topology of
a phylogenetic tree. The parent branch length of a clade can be described either with
the 'branch_length' element or the 'branch_length' attribute (it is not recommended to
use both at the same time, though). Usage of the 'branch_length' attribute allows for a
less verbose description. Element 'confidence' is used to indicate the support for a
clade/parent branch. Element 'events' is used to describe such events as
gene-duplications at the root node/parent branch of a clade. Element 'width' is the
branch width for this clade (including parent branch). Both 'color' and 'width' elements
apply for the whole clade unless overwritten in-sub clades. Attribute 'id_source' is
used to link other elements to a clade (on the xml-level).

Complex Type Information

Model

Attributes

QName Type Fixed Default Use Inheritable Annotation
branch_length xs:double optional
collapse xs:boolean optional
id_source phy:id_source optional

Used By

Source

<xs:complexType name="Clade">
  <xs:annotation>
    <xs:documentation>Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree. The parent branch length of a clade can be described either with the 'branch_length' element or the 'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the 'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).</xs:documentation>
  </xs:annotation>
  <xs:sequence>
    <xs:element name="name" type="xs:token" minOccurs="0"/>
    <xs:element name="branch_length" type="xs:double" minOccurs="0"/>
    <xs:element name="confidence" type="phy:Confidence" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="width" type="xs:double" minOccurs="0"/>
    <xs:element name="color" type="phy:BranchColor" minOccurs="0"/>
    <xs:element name="taxonomy" type="phy:Taxonomy" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="sequence" type="phy:Sequence" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="events" type="phy:Events" minOccurs="0"/>
    <xs:element name="binary_characters" type="phy:BinaryCharacters" minOccurs="0"/>
    <xs:element name="distribution" type="phy:Distribution" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="date" type="phy:Date" minOccurs="0"/>
    <xs:element name="reference" type="phy:Reference" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="property" type="phy:Property" minOccurs="0" maxOccurs="unbounded"/>
    <xs:element name="clade" type="phy:Clade" minOccurs="0" maxOccurs="unbounded"/>
    <xs:any minOccurs="0" maxOccurs="unbounded" processContents="lax" namespace="##other"/>
  </xs:sequence>
  <xs:attribute name="branch_length" type="xs:double"/>
  <xs:attribute name="id_source" type="phy:id_source"/>
  <xs:attribute name="collapse" type="xs:boolean"/>
</xs:complexType>