squash

squash performs squash clustering.

usage: squash [options] placefiles

Options

--point-mass	Treat every pquery as a point mass concentrated on the highest-weight placement.
--pp	Use posterior probability for the weight.
-c	Reference package path.
--seed	Set the random seed, an integer > 0. Default is 1.
--min-fat	The minimum branch length for fattened edges (to increase their visibility). To turn off set to 0. Default: 0.01
--total-width	Set the total pixel width for all of the branches of the tree. Default: 300
--width-factor	Override total-width by directly setting the number of pixels per unit of thing displayed.
--node-numbers	Put the node numbers in where the bootstraps usually go.
--out-dir	Specify the directory to write files to.
--prefix	Specify a string to be prepended to filenames.
-p	Exponent for KR integration, i.e. value of p in Z_p. Default 1.
--normalize	Divide KR by a given value. Legal arguments are “tree-length”.
--bootstrap	the number of bootstrap replicates to run
-j	The number of processes to spawn to do bootstrapping. default: 2
--tax-cluster	Perform taxonomic clustering rather than phylogenetic.Specify “unit” or “inv” for the two different modes.
--pre-round	Apply rounding with 3 sig figs and cutoff 0.01 to each placerun before clustering
--unitize	Unitize masses after bootstrap resampling

Details

Perform squash clustering.

Bootstrapping is performed by resampling directly on placements. Note that the bootstrap values for clustering are calculated in a rooted way. That means that you may observe different bootstrap values on either side of the root, especially if a whole clade from one side of the root likes to flip to a location distal to the clade on the other side of the root.