bary¶
bary draws the barycenter of a placement collection on the reference tree.
usage: bary [options] placefile[s]
Options¶
| -c | Reference package path. |
| --point-mass | Treat every pquery as a point mass concentrated on the highest-weight placement. |
| --pp | Use posterior probability for the weight. |
| -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. |
| --node-numbers | Put the node numbers in where the bootstraps usually go. |
Details¶
Calculate the center of mass of the placement distribution and write it out to a phyloXML file for viewing. When several place files are given, calculate the barycenter for each, and mark them on the same tree. Because phyloxml isn’t actually designed to show points on the tree, the phyloXML is a kluge for the time being– using “speciation” and “duplication” tags.