pxrlt and pxrmt doesn't output tip name with "-" correctly

[fkyeeb]

for example if the tip name is "Van-royena_castanosperma", the tip name in the output tree will be "'Van-royena castanosperma'". The underscore will be removed and single quotation marks will be added to either side of the name.

[josephwb]

Can you please provide input files and expected output?

[josephwb]

Actually, this is a "feature". Names that contain Nexus-illegal characters (()[]{}/\,;:=*'"`+-<>) should be single-quoted (otherwise it can cause troubles with various Nexus-compliant tree readers). Underscores are considered as space-characters in unquoted labels, and so are replaced by literal spaces in the quoted label.

Does that make sense.

[fkyeeb]

Yes! Thank you. Then what should I do if I would like the tip name to not change after using phyx, when the tip name has to contain Nexus-illegal characters?

[josephwb]

Any name you want to conserve literally, just surround with single quotes. So in your example above, replace:

Van-royena_castanosperma

with

'Van-royena_castanosperma'

and everything should work as expected. Sorry for the headache; some programs are Nexus-compliant, others partially so. :)

[fkyeeb]

Thank you for helping!