Format conversion


See the HoneyBadgerFish for full documentation of the NeXML to NexSON conversion convention.


$ python scripts/nexson/ input -e 1.2 -o output

will read NeXML or NexSON as input and produce version 1.2 of the honeybadgerfish NexSON and

$ python scripts/nexson/ input -e nexml -o output

to write NeXML.

The -h command line flag reports more details about the arguments.


$ python scripts/nexson/ -h

Explains the options for running a NexSON to newick converter. A tree’s ID can be specified, and the field used to label the tips can be chosen from the command-line options.