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necrolyte2 / beast-mcmc

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Having taxon sets defined without heights when using a user starting tree causes parsing issues. #728

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Load a starting tree in BEAUti and create some taxon sets. The XML produced 
will take the form:

    <!-- Construct a starting tree that is compatible with specified clade heights-->
    <rescaledTree id="startingTree">

        <!-- The user-specified starting tree in a newick tree format.               -->
        <newick usingDates="false">
                    ---tree here----
        </newick>
        <clade>
            <taxa idref="test"/>
        </clade>
        <clade>
            <taxa idref="test2"/>
        </clade>
    </rescaledTree>

This will fail to load because the 'clade' elements don't have heights. If 
heights are specified in the taxon set table then this will work fine.

Possible solutions:

Don't write <clade> elements unless heights are specified (or monophyly 
enforced?).

Original issue reported on code.google.com by ramb...@gmail.com on 13 Mar 2014 at 4:26

GoogleCodeExporter commented 9 years ago 
BEAST now reads <clade> elements without heights (checks they exist in the 
tree). BEAUti doesn't generate <clade> elements for taxon sets without dates or 
specified as monophyletic.

Original comment by ramb...@gmail.com on 5 Aug 2014 at 8:09