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http://www.beast2.org/wiki/index.php/BEAST_Features
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Hi Walter
I was following the Phylogeography example that is on the BEAST2 page. I installed the add-ons BEAST_CLASSIC and BEASTii. I then click the + at the bottom left of the partition tab and choo…
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MTT currently shares namespaces with BEAST. This is generally a bad thing, but can also cause specific problems such as BEAST picking up MTT packages during its own unit tests if MTT is installed on …
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Often you want to start with a reasonable tree, and so a UPGMA tree is a good starting place. However UPGMA trees are in units of substitutions. If your MCMC is on a time-tree in units of years or mil…
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Create wiki for Developer's Rules
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BEAUti produces XML which results in messages like
"Element tree found with idref='Tree.t:meta41sp13g_cod3'. All other attributes are ignored."
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update Java doc for 2.1.3
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snap.MCMC has some functionality we might want to have in beast.core.MCMC (so snap.MCMC can be retired)
- time out: stop running after a specified nr of seconds.
- sample initial state from the prior.…
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Some users cannot get the package manager to get access to the packages.xml file (e.g. https://groups.google.com/forum/#!topic/beast-users/Gc-3rGcIw8w). A procedure should be in place to allow manual …
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Dear Walter,
Can you add this as an issue on BEAST2 google code site? The fix should be to automatically create the directory if it doesn't exist (and report doing so on the terminal).
Cheers
Alexei…