adcl calculates ADCL for each pquery in a placefile.
usage: adcl [options] placefile
| --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. |
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.