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similar to Issue 485: BEAUti trunk: tree prior is locked at Coalescent Constant
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Original issue reported on code.google.com by `dong.w.xie@gmail.com` on 8 Nov 2011 at 11:30
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If you are receiving IM messages with grip, from popular apps like IM+ or
Beejive, you get ALOT of grip boxes, one everytime your friend presses send.
Could it be possible in this situation to …
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BEAUti Generates the wrong taxa set for the starting tree
is for the full set.
I unlinked all partitions, but beauti generated just one combined taxa set.
Consequently beast fails.
…
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An unnecessary rate is generated
The non changing clock.rate is in the log
the "constant.popSize" parameter has an operator and is in the prior - wrong
bmPrior="true" - no longer correct, defa…
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Currently, BEAUti generates uniform priors between bounds by setting upper and
lower attributes on the parameters. This should change to adding a
element to the priors block so all priors are e…
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An unnecessary rate is generated
The non changing clock.rate is in the log
the "constant.popSize" parameter has an operator and is in the prior - wrong
bmPrior="true" - no longer correct, defa…
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What steps will reproduce the problem?
1. run a beast file with -seed 0
2.
3.
What is the expected output? What do you see instead?
Please use labels and text to provide additional information.…
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Hi Walter,
I have been trying to get BEAST v1.5.1 to work and am having problems. I
have tested it using three .xml files that have all worked fine in v1.4.8.
These three files differ only in th…
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If a tree prior is selected over multiple unlinked trees then for most models a
separate coalescent likelihood is generated for each tree with a shared
coalescent model. For ESB however a multi …
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What steps will reproduce the problem?
1. Initialize a tree with UPGMA
2. Calculate initial density of the coalescent
This bug was introduced in revision 811 in Coalescent.java lines 101-106. I …