beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
BEAUti generates incorrect up down operator of clock rate and tree for multi-alignment Load multi-alignment, link clock rate but unlink trees, make clock rate be estimated, and then the xml...
The work around mentioned in #749 on BEAUti's about menu gives a non-standard about menu. It would be nice to have a standard about menu interface for BEAUti using Java...
From: Ahmed Magdy Moustafa I would like to use just polymorphic sites (1473) with associated tip dates and the SNP ascertainment bias correction in BEAST2. Are there specific steps to...
It is well-known amongst the development team that BEAUti can become "confused" - i.e. the BEAST model it holds in memory can become corrupted, or the model is in some...
From: Ingi Agnarsson I'm trying to get taxon sets into Beauti. I have 563 taxa so defining sets within beauti is painstaking, as is listing taxon names in each set...
Distribution always had these methods: List getArguments() List getConditions() void sample(State state, Random random) but these were mostly not implemented, nor used. Will be good to have a way to...
If Node.setRight(Node rightChild) is called on a node with no children it will result in getChildCount() returning 2 when there is only one non-null child node. Should we consider failing...
I have a BranchRateModel which takes a LogNormal distribution as input. The mean of the distribution is constant and the standard deviation (the "S" parameter) is estimated. There is a...
In a *BEAST analysis, a calibration can be populated with IDs that have numbers attached, see https://groups.google.com/forum/#!topic/beast-users/gwK18aHIFr8 Also SBI does not seem to pick up lower bounds on such calibrations...
Tired of generating issues? Let the machine do the work. Run findbugs (http://findbugs.sourceforge.net) and select one of the 1125 bugs. Some are false positives, but I think the code could...