:tocdepth: 3

.. _rppr_infer:

=====
infer
=====

`infer` infers classifications of unclassified sequences in a reference package.

::

  usage: infer [options] -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.
--csv  Output the results as csv instead of a padded matrix.
-j  The number of processes to run pplacer with. default: 2
-p  Calculate posterior probabilities when doing placements.
--placefile  Save the placefile generated by running pplacer to the specified location.

Details
=======

Take any unclassified sequences in the reference package and place them with
pplacer against the classified sequences in the reference package. The result
is a table of the suggested classifications of these sequences:

============ ===========
Column name  Description
============ ===========
seq_name     The name of the sequence.
new_taxid    The actual suggested tax_id.
new_name     The name of the suggested tax_id for this sequence.
============ ===========