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beast-dev / beast-mcmc

Bayesian Evolutionary Analysis Sampling Trees
http://beast.community
GNU Lesser General Public License v2.1
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BEAUti doesn't generate correct relative rates for amino acid partitions. #1051

Closed rambaut closed 4 months ago

rambaut commented 5 years ago

BEAUti doesn't add 'nu' relative rates into amino acid siteModel elements

rambaut commented 4 months ago

To reproduce - load two amino acid partitions, unlike substitution models. BEAST gives the following on the generated XML:

Error in input BEAST XML file, Issue_#1051.xml:
Object with idref=part1.nu has not been previously declared.
rambaut commented 4 months ago

Need to add:

        <relativeRate weight="2.0">
            <parameter id="part1.nu" value="0.5" lower="0.0" upper="1.0"/>
        </relativeRate>

into the site models

rambaut commented 4 months ago

Fixed