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This release adds the ability to specify conversion-free loci: loci on which recombination is not allowed.
Currently, disabling conversions on a locus requires editing the BEAST XML file. Happily the modification is trivial. Simply locate the opening tag for the locus you wish to disable conversions on, for instance
<locus id="locus.partition_name" spec="bacter.Locus">
partition_name is the name of the alignment corresponding to the locus. Then just add the attribute
<locus id="locus.partition_name" spec="bacter.Locus" conversionsAllowed="false">
The analysis should now avoid proposing conversions on this locus.