beast2
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CompEvol
Bayesian Evolutionary Analysis by Sampling Trees
Adding a line like: `xml = xml.replaceAll("\\n\\s*\\n", "\n");` directly after `xml = findPlates(xml2)` should fix it.
Right now there is no (single-liner) way of checking if a Parameter is being estimated or not. A default method in Parameter like: ``` default boolean isEstimated() { // loop...
Hi, I am trying to run the beast2 and i was confused about incorporating the tip date information in some cases in my dataset. I have followed this link for...
Hi, While packaging beast2 for Debian, I focused on the build-time tests you provide and I noticed the following issues : - testBeautiSubTemplateIfElement, testBeautiSubTemplateCombined and testBeautiSubTemplateIfMultipleElement output things like `expected:`...
Hi, I ran AIM but I could not summarize the species tree using the “AIM species tree annotator” app. This application is not listed in the AppLauncher. Does anyone know...
For likelihoods that depend on tree orientation, loggers that sort the tree in state break likelihood comparisons in store/restore. Solution: copy the tree as its being logged, sort the copy...
The core code to parse ranges in filtered alignments is https://github.com/CompEvol/beast2/blob/1ba8d2bff70d4fe69b355c2c3670f32295a88e6e/src/beast/evolution/alignment/FilteredAlignment.java#L100-L107 In that code, the comment uses a forward slash, but the code splits according to a backward slash. //...
Hi, In the test file ExampleXmlParsingTest.java, org.fest.swing.security.ExitException is imported whereas it is not used : ExitException is defined later as overriding java.lang.SecurityException. This import can thus be removed. Best, Pierre
Hi - I am experiencing the following issue: I initially set site models for each of my 32 partitions in beauti. I then set a lognormal clock model on the...
Once you link models, sites and/or trees in BEAUTI 2.6.3 for OS X, it's not possible to unlink them without losing partitions. As an example, if I try to unlink...
