Guy Baele

When simulating data under a codon MMM, the simulated sequences look as follows: TTA0AAT0GTA0TCT1 ... While this is very useful for parsing output annotated on trees, it prevents immediately using...

Checkpointing does not seem to work with Markov-modulated models

1

The state file generated contains entries such as: parameter treeModel.rootHeight 1 174.13024862028956parameter 0 1 8.413698630136878parameter ... These '174.13024862028956parameter' entries can obviously not be parsed correctly upon loading the state file.

There is a problem when assigning tip date uncertainty to taxa in the Tips panel in BEAUti, but only when you first sort the sequences (for example, according to their...

Importing partition information in BEAUti 1.10.x

1

From an e-mail I received (sounds like a bug as it worked in previous versions): When you want to import a nexus file with protein sequence data and partition information...

allMus with unequal weights clashes with Dirichlet prior

5

For example, the Ebola data set has 4 weights in total, with the weight for the intergenic region partition differing from the 3 weights of the codon positions. A deltaExchange...

Need scaled logit for generalized stepping-stone sampling?

1

Currently, log transformation is used for positive parameters and logit for probabilities (like the base frequencies being estimated). The relative rate parameters are quite similar to the base frequencies, but...

HPM operators in BEAUti

1

Upon creating HPMs in BEAUti, the corresponding operators on the HPM parameters (i.e. normalNormalMeanGibbsOperator and normalGammaPrecisionGibbsOperator) do not appear in the Operators panel and hence their weights cannot be modified...

Add half a year to sampling date when performing tip date sampling

1

When setting up tip date sampling in BEAUti, half a year is being added implicitly to the sampling date. However, this change is not reflected in BEAUti, nor in the...

BEAUti weight for AVMVN transition kernel

2

Currently, the weight for the AVMVN transition kernel is set to 'treeWeights', i.e. 15.0. Should probably use our suggestion from the paper, where we set the weight of the AVMVN...

Currently, performing BSSVS on a skygrid+covariates model involves defining a productParameter first: ```xml ``` However, it's not possible to set the value of a productPatameter as there's no telling what...