rarefact

rarefact calculates phylogenetic rarefaction curves.

usage: rarefact [options] placefile

Options

--pp	Use posterior probability for the weight.
-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.
--variance	Calculate variance of phylogenetic entropy.
--weight-as-count
	Interpret (integer) weights on pqueries as counts.
-k	The highest value of k to calculate.

Details

Calculate phylogenetic rarefaction curves.

For every k \in [2, n], where n is the number of pqueries in a placefile, subsample the given placefile to contain every combination of k pqueries and calculate the mean and variance of phylogenetic divesity for all of these subsampled placefiles.

The rooted_mean and rooted_variance columns are respectively the mean and variance of the phylogenetic diversity only requiring mass on the distal side of the edge (which normally requires mass proximal and distal to the edge).

For more details, see Nipperess and Matsen.