NexSON/NeXML

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

Usage

$ python scripts/nexson/nexson_nexml.py 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/nexson_nexml.py input -e nexml -o output

to write NeXML.

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

NexSON/Newick

$ python scripts/nexson/nexson_newick.py -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.