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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 --cutoff level
  • round the branch lengths to --sig-figs significant figures
  • group placements that are identical after this process.