:tocdepth: 3

.. _guppy_adcl:

====
adcl
====

`adcl` calculates ADCL for each pquery in a placefile.

::

  usage: adcl [options] placefile

Options
=======

--pp  Use posterior probability for the weight.
--min-distance  Specify the minimum distance to leaves to report
--max-matches  Only report the deepest N placements
--include-pendant  Include pendant branch lengths in distance calculations.
--no-collapse  List all of the names per pquery instead of just one.
-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.
--no-csv  Output the results as a padded matrix instead of csv.

Details
=======

This subcommand spits out a three column CSV file such as::

    GLKT0ZE02ICPDW,0.243279,1
    GLKT0ZE02GLVHA,0.243157,3
    GLKT0ZE02HFAHN,0.242753,1
    GLKT0ZE02GI5BZ,0.032986,1
    GLKT0ZE02F6DFD,0.023905,2

where the first column is placement name, second column is distance to closest leaf, and third column is multiplicity.
Pqueries are sorted by distance to leaf.