Creates the 'tree' section of a BEAST2 XML parameter file, which is part of a 'state' section, without being indented, when there is no tip-dating

no_taxa_to_xml_tree(inference_model, id = "deprecated")

Arguments

inference_model

a Bayesian phylogenetic inference model. An inference model is the complete model setup in which a site model, clock model, tree prior and more are specified. Use create_inference_model to create an inference model. Use check_inference_model to check if an inference model is valid. Use rename_inference_model_filenames to rename the files in an inference model.

id

an alignment's IDs. An ID can be extracted from its FASTA filename with get_alignment_ids_from_fasta_filenames)

Value

the random phylogeny as XML text

Details

The tree tag has these elements:


   <tree[...]>
       <taxonset[...]>
       [...]
       </taxonset>
    </run>

Author

Richèl J.C. Bilderbeek