kche309

@ddkapan I have been working on an error model framework for beast2 which includes a nucleotide sequencing error model (in testing phase). It is slightly different from the Oxford paper...

Hi @ddkapan, We're currently working on getting the user interface working (Beauti). There's currently a bug in the templates which means configuring these types of analyses will require manual editing...

Hi @ddkapan just a brief update on expected timeframe for the PMD model. We will schedule to implement this in April. I will let you know once an early version...

@ddkapan Hi work is in progress for this model on branch https://github.com/bioDS/beast-phylonco/tree/PMDErrorModel The main source code is in [PMDErrorModel.java](https://github.com/bioDS/beast-phylonco/blob/PMDErrorModel/phylonco-beast/src/main/java/phylonco/beast/evolution/errormodel/PMDErrorModel.java) This is pending ~~a fix on the Gradle build file~~ testing...

@ddkapan I have a few quick questions about your data. (1) Do you have a mix of extant species and museum fossil samples? (2) Would it be correct to assume...

@ddkapan A brief update, I've added an exclusion option (for excluding certain taxa from the PMD error model, e.g. extant species). Main code is now complete, I will be adding...

Note that currently there are log files are handled differently through the GUI LPhy Studio compared to command-line slphy. Command line and alignments: `ValueFileLoggerListener` and `ValueFormatHandler` -- old implementation using...

Thanks for your helpful suggestion, the R style syntax looks like a good approach as well. We will be adding this feature in the future releases.

See main method in https://github.com/LinguaPhylo/linguaPhylo/blob/master/lphy-studio/src/main/java/lphystudio/app/NarrativeCreator.java Add this as a file menu item to export narratives as HTML or markdown.