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">
	<header>
		<seq>
			<name>A sequence name!</name>
		</seq>
		<seq>
			<name>Another name with a \< symbol</name>
			<cmt>This sequence has a comment</cmt>
		</seq>
		.
		(145 <seq>)
		.
	<header>

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

	<Labels>   (Labels are optional)
	<label x="31" y="13" w="30" h="12">The name of the label</label>
		.
		.
	</Labels>
	<matrix>
		<block x="0" y="0" width="1301" height="147">
			AAAAGTGATAACTTTCAAATTCAGAGAAACCC..CGGAATTAATAAAAA---TGGGCGA
			CACAGA  (...)  CCCCAGTCATCT-AATAAAAT----------------GAGGATGGA
			---ACA--TTGG (...) AAATGGTC\FF
			CAAATC-A-CCCAC--TCCATTGTCTGATAG-----ATCTTTT----AAAGAAC???TGA
			ATCCCCAAAA------ (...)---------GGCCTATTTT--------------CCAT\FF
			.
			(145 lines)
			.
		</block>
	</matrix>
</alignment>
</phyde>

A few additional remarks are necessary:

alignment

• datatype may be "dna" or "amino"
• The version must be "0.98"
• The offset=-1 in the alignment item is to assign column no 1 to the first column.

header

• The number of sequences (=number of <seq>) must be as given by height in alignment.
• In general, you should be careful with non-alphanumeric characters in name, label, etc. If in doubt, write \c instead of c, especially \< for <

block

• width and height must be the same as in alignment. x and y must be "0".
• Whitespaces, i.e newline, return, tabulator and space, are ignored. The following ASCII characters are allowed in the sequence data:

  ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz 0123456789 !"#$%&'()*+,-/:;=>?@[]^_`{|}~

• After each line in the block data (i.e. after width non-white characters) the special symbol \FF must appear. The number of these lines must be as given by height

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.