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We're getting beast2 run failures in a multi-user environment because of the uncommented debugging code left in a release package even though there is a note in BeastLauncher.java that says
" …
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In BEAUti priors tab
gamma [alpha (shape)=0.001 and a beta (scale)=1000
Beauti displays 8.73e-10 for the median. In R
> qgamma(.5, shape=.001, scale=1000)
> [1] 5.244206e-299
Why the discrepancy?
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Equal-tailed intervals can be quite different to HPDs.
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I've been trying to compile Hyphy using the provided instructions to install PoMo.
`cmake ./` fails with the error:
"Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Tes…
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The JSON library used has a license that prevents BEAST to be made into a Debian package (https://wiki.debian.org/qa.debian.org/jsonevil). There are alternatives like json-simple (http://code.google.c…
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```
What steps will reproduce the problem?
1. Run the attached XML
What do you see instead?
Parsing XML file: pp.rag.beast2.xml
Read alignment, 'alignment':
Sequences = 9
Sites = 4753
Dataty…
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On Windows, with STACEY installed, the STACEY template shows up but Standard and StarBeast templates are missing from the File/Templates menu. They can be used by finding them through the File/Templat…
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I have been unable to use the "read from file" option to load sampling dates. Please provide an example file or easier to parse instructions.
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We should gather data about the benchmark environment like:
- OS: Name and Version
- CPU: At least number of cores, but having information about the model and its microarchitecture would be great, num…
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I haven't had a chance to investigate fully to figure out the underlying cause, but reading the tree files generated directly from treeannotator mixes up the tip labels (they are assigned to the wron…