PDE file format

The .pde files are XML files, optionally GZIP compressed. If you want to write your data in this format, you should read this documentation. Please note, that PhyDE does not fully implement all features of XML. For example, comments must not contain a >-Symbol. Therefore you should always check, if PhyDE really interprets your data correctly. If you implement only the following minimal features, no problems should occur.

This is a simple example of a .pde file:

<?xml version="1.0" standalone="no"?>
<!-- A completely unnecessary comment -->  (Comments must not contain > !)
<phyde version="0.98">
<alignment datatype="dna" width="1301" height="147" offset="-1">
			<name>A sequence name!</name>
			<name>Another name with a \< symbol</name>
			<cmt>This sequence has a comment</cmt>
		(145 <seq>)

	<CharSets>   (Character sets are optional)
	<charset name="First set">11-22 31-48 56-72</charset>

	<Labels>   (Labels are optional)
	<label x="31" y="13" w="30" h="12">The name of the label</label>
		<block x="0" y="0" width="1301" height="147">
			ATCCCCAAAA------ (...)---------GGCCTATTTT--------------CCAT\FF
			(145 lines)

A few additional remarks are necessary:




The label in the example is positioned at column 32 in the 14th sequence, i.e. counting starts at 0.

Please note that the above example is simplified but working. PhyDE implements much more features, including checksums, run-length encoding in the <block> item, Taxon sets, links to external files, etc. They are not documented here, because they might be implemented differently in the future.