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.. _rppr_ref_tree:

========
ref_tree
========

`ref_tree` writes a taxonomically annotated reference tree and an induced taxonomic tree.

::

  usage: ref_tree -o my.xml -c my.refpkg

Options
=======

-c  Reference package path. Required.
-o  Specify the filename to write to.
--out-dir  Specify the directory to write files to.
--prefix  Specify a string to be prepended to filenames.
--node-numbers  Put the node numbers in where the bootstraps usually go.
--painted  Use a painted tree in place of the taxonomically annotated tree.
--rank-colored  Include a tree for each rank with taxonomic annotations on every edge.