ref_tree writes a taxonomically annotated reference tree and an induced taxonomic tree.
usage: ref_tree -o my.xml -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. |
| --node-numbers | Put the node numbers in where the bootstraps usually go. |
| --painted | Use a painted tree in place of the taxonomically annotated tree. |
| --rank-colored | Include a tree for each rank with taxonomic annotations on every edge. |