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.