beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
Though the public release is still a bit off since we need to decide what will be included, this is a catch all issue for dealing with anything to do...
Sequencing error models (and post-mortem damage models) are implemented in BEAST1. See http://mbe.oxfordjournals.org/content/26/2/245.full Users would like this ported to BEAST2.
Stderr should be empty for a run, where no error was encountered. Currently, some extra information is printed to stderr. These are not warnings, these are not errors, just messages...
Hey team- I've followed the previous threads (#478) on BEAUti adding 1s to taxon IDs, and seen the solution to change the .xml file as so: replace taxon id="668666_Onth_long_" spec="Taxon”/...
Keeping package loading working for both java 8 and java 9+ turns out to be quite hard work, and the current solution (start a Launcher that kicks of a second...
The Yule prior produces a warning about a missing MRCA prior on the root, even when the prior is present because `validateInputs()` is called before `initAndValidate()` is called, so the...
I am trying to resume an interrupted run on v2.6.3 on Windows and am getting this error: Appending file C:\Users\Kendall\Desktop\beast-copy\concatenated-alignment-fossils.log File error: C:\Users\Kendall\Desktop\beast-copy\$marmotTrees2.trees -> C:\Users\Kendall\Desktop\beast-copy\$marmotTrees2.trees: The process cannot access the...
95% HPDs are constructed as follows: given N samples, x_1…x_N sorted by value, put a moving window of size n=(N-1)*95/100 over the sorted sequence and report the x_i and x_{i+n}...
Tested with the following tree `((4:0.150558013,5:0.150558013)7:1.154521107,(((2:0.2610234442,3:0.2610234442)9:0.02397655557)10:0.006852994,1:0.2918529938)8:1.013226126)6;` BEAST2 runs fine with it but restoring state fails with a NullPointerException As far as I can tell the issue comes from `Tree.assignFrom`, which...
`packagemanager -add ORC` gives a `javax.net.ssl.SSLHandshakeException`. The package manager in BEAUti BEAUti still lists all packages, but when you try to install a message saying: "Install failed because: java.security.cert.CertificateException: No...