FAQ for Phylomatic database

$Revision::        $
$Date::            $

  Q: Why won't the megatrees (e.g., R20081027.new) open in TreeViewX?

    A: The phylomatic database allows single daughter nodes in Newick:
    ((A,B)C)D which are also allowed by the Newick standard.  TreeView
    can also handle these, but seems not to like it when the files are
    large.  The single daughter nodes can be cleaned out using
    phylocom, e.g.:

      $ phylocom phylocom cleanphy -e -f R20081027.new > clean.new

    The resulting file will open in TreeView.  I have found that ATV
    can open the files directly.

  Q: Are the XML files valid?

    A: Cam regularly runs: jing -c pmmd/pmmd.rnc trees/*.xml
    But... the XML files are hand coded, so errors may creep in once in a while.