update PAML test result generator to support PAML 4.7
add PAML 4.7 test results
Will add support for NeXML trees to Bio.Phylo. Updating _io.py.
Adding stub write/parse methods and NeXML parser generated by generateDS.py.
Adding basic NeXML tree parser.
Updating copyright statement.
Use otu instead of label for taxon label.
Adding comments.
Most of the NeXML writer has been implemented, with TODOs marking what still needs to be done.
NeXML parser/writer with basic support for NeXML nodes, edges, and otus is now functional.
Using ElementTree parser instead of generateDS.py parser so that output will be correct and make appropriate use of namespaces.
Use xml.dom.minidom to re-parse NeXML output and pretty print the result.
Add xsi:schemaLocation.
Enable passing in keyword args to parse in Bio.Phylo.convert.
Minor correction to copyright statement.
Minor changes so that output passes nexml.org validation. OTUs block should be first, and version should be 0.9.
Use ET.iterparse to enable parsing of large trees without running out of memory.
NeXML trees/clades use their own subclass of BaseTree.Tree and BaseTree.Clade instead of Newick.Tree and Newick.Clade.
Updating cdao prefix URI.
Filling in relative URI for nexml schema.