:tocdepth: 3

.. _rppr_convexify:

=========
convexify
=========

`convexify` identifies minimal leaf set to cut for taxonomic concordance.

::

  usage: convexify [-c my.refpkg | --tree my.tre --colors my.csv]

Options
=======

-c  Reference package path. Required.
--node-numbers  Put the node numbers in where the bootstraps usually go.
--tree  A tree file in newick format to work on in place of a reference package.
--colors  A CSV file of the colors on the tree supplied with --tree.
-t  If specified, the path to write the discordance tree to.
--cut-seqs  If specified, the path to write a CSV file of cut sequences per-rank to.
--alternates  If specified, the path to write a CSV file of alternate colors per-sequence to.
--check-all-ranks  When determining alternate colors, check all ranks instead of the least recent uncut rank.
--all-alternates  When determining alternate colors, ignore the taxononomy and show all alternates.
--cutoff  Any trees with a maximum badness over this value are skipped. Default: 12.
--limit-rank  If specified, only convexify at the given ranks. Ranks are given as a comma-delimited list of names.
--timing  If specified, save timing information for solved trees to a CSV file.
--rooted  Strictly evaluate convexity; ensure that each color sits in its own rooted subtree.
--naive  Use the naive convexify algorithm.
--no-early  Don't terminate early when convexifying.

Details
=======


``convexify`` applies an exact dynamic program to identify leaves of a phylogenetic tree that don't agree with their taxonomic labels.
You can read more in the announcement_ or the paper_.

You can either specify a reference package or a tree and a CSV file of colors.
The CSV file is formatted as follows::

  leaf_name1,color1
  leaf_name2,color2

where the colors are just strings.

Note that ``--no-early`` and ``--naive`` don't change the results.
They just (much) run more slowly for all but the most trivial problems.


.. _announcement: http://matsen.fhcrc.org/general/2011/09/27/convexify.html
.. _paper: http://arxiv.org/abs/1109.5423