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evolvedmicrobe / beast-mcmc

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NexusImporter and Markov Jumps CJH to tree #727

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run a Markov Jumps analysis that maps the complete jump history to the 
relevant branches - add useUniformization="true" saveCompleteHistory="true" 
logCompleteHistory="true" compactHistory="true" as attributes to 
<markovJumpsTreeLikelihood>, then add the following to <logTree>:

      <trait name="history_all" tag="history_all">
        <markovJumpsTreeLikelihood idref="Country.treeLikelihood"/>
      </trait>

2. Open a posterior tree with FigTree (or anything else that uses NexusImporter)

NexusImporter doesn't know to escape certain characters that the CJH format 
uses, so the result is a mess.

Original issue reported on code.google.com by mdhall272 on 11 Mar 2014 at 11:23

GoogleCodeExporter commented 9 years ago 
... where "Country" is the name of your trait, of course...

Original comment by mdhall272 on 11 Mar 2014 at 11:24

GoogleCodeExporter commented 9 years ago 
Seems to have been fixed without me noticing. Sorry.

Original comment by mdhall272 on 23 Apr 2014 at 12:00