BEAUti options are settings that differ between BEAUti version. The use of these options is mostly for testing older versions Whatever option chosen here, the created XML file will be valid.
create_beauti_options( capitalize_first_char_id = FALSE, nucleotides_uppercase = FALSE, beast2_version = "2.4", required = "", sequence_indent = 20 )
must the ID of alignment start with a capital? TRUE if yes, FALSE if it can be left lower case (if it is lowercase)
must the nucleotides of the DNA sequence be in uppercase?
the BEAST2 version
things that may be required,
the number of spaces the XML
lines are indented
a BEAUti options structure