Order of elements in phyloXML

Since the validity of phyloXML documents is enforced by a XSD Schema, the order of elements matters (for more information and discussions, see http://www.w3schools.com/Schema/schema_complex_indicators.asp).

The current (as of 9 September 2010) BioPerl implementation of the phyloXML format unfortunately produces output with incorrect element order. For Archaeopteryx users a temporary “solution” is to turn off XSD-based validation, with the following line in the Archaeopteryx  configuration file:

validate_against_phyloxml_xsd_schema: false

Examples of proper order of sub-elements

For <clade> the order of sub-elements is:

1. <name>
2. <branch_length>
3. <confidence>
4. <width>
5. <color>
6. <taxonomy>
7. <sequence>
8. <events>
9. <binary_characters>
10. <distribution>
11. <date>
12. <reference>
13. <property>
14. <clade>

For <sequence>, the order is:

1. <symbol>
2. <accession>
3. <name>
4. <location>
5. <mol_seq>
6. <uri>
7. <annotation>
8. <domain_architecture>

For <taxonomy>, the order is:

1. <id>
2. <code>
3. <scientific_name>
4. <authority>
5. <common_name>
6. <synonym>
7. <rank>
8. <uri>

Needless to say, not all sub-elements have to appear, but if they do, they have to appear in proper order.