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.