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katylettuce / beast-mcmc

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Code generated by BEAUti for substitutions trees doesn't load into BEAST #631

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
When saving trees with branch lengths in substitutions the following error 
comes up:

Error parsing '<logTree>' element with id, 'substTreeFileLog':
To log trees in units of substitutions a BranchRateModel must be provided

The logTree element is output from Beauti.

        <logTree id="substTreeFileLog" logEvery="1000" nexusFormat="true" fileName="Tree.(subst).trees" branchLengths="substitutions">
            <treeModel idref="treeModel"/>
            <trait name="rate" tag="rate">
                <discretizedBranchRates idref="branchRates"/>
            </trait>
        </logTree>

The fix is to alter the tree logger parser to accept a trait named rate as well 
as a BranchRateModel.

Original issue reported on code.google.com by ramb...@gmail.com on 29 May 2012 at 5:38

GoogleCodeExporter commented 9 years ago

Original comment by ramb...@gmail.com on 3 Aug 2012 at 3:08