pdprune prunes the tree to maximize PD.
usage: pdprune [options] tree
| -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. |
| --cutoff | Specify the maximum branch length to be trimmed. |
| --leaves | Specify the maximum number of leaves to leave un-trimmed. |
| --names-only | Only split out a list of names, rather than names and PD decrease. |
| --unsafe | Don’t perform internal checks. |
| --never-prune-from | |
| Provide a file containing sequence names that will not be pruned. | |
| --never-prune-regex-from | |
| Provide a file containing regular expressions; sequence names matching one of these will not be pruned. | |