:tocdepth: 3

.. _guppy_squash:

======
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.


.. _squash clustering: http://arxiv.org/abs/1107.5095