infer infers classifications of unclassified sequences in a reference package.
usage: infer [options] -c my.refpkg
| -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. |
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. |