round¶
round clusters the placements by rounding branch lengths.
usage: round [options] placefile[s]
Options¶
| --out-dir | Specify the directory to write files to. |
| --prefix | Specify a string to be prepended to filenames. |
| --sig-figs | Set the number of significant figures used for rounding. Specify 0 for no rounding. Default: 3. |
| --cutoff | Set the rounding inclusion cutoff for the ML weight ratio. Default: 0.01. |
Details¶
This subcommand provides very basic “clustering” functionality. This is not meant to derive “species level” or analogous groupings, but rather to group placements which will have essentially identical impact in a guppy analysis.
Rounding is done as follows:
- throw out the placement mass below the
--cutofflevel- round the branch lengths to
--sig-figssignificant figures- group placements that are identical after this process.