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Conversion-free loci
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@tgvaughan tgvaughan released this 24 Apr 16:16
· 25 commits to master since this release
v2.1.0
622ba17

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">

where partition_name is the name of the alignment corresponding to the locus. Then just add the attribute conversionsAllowed="false":

 <locus id="locus.partition_name" spec="bacter.Locus" conversionsAllowed="false">

The analysis should now avoid proposing conversions on this locus.

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