fat makes trees with edges fattened in proportion to the number of reads.
usage: fat [options] placefile[s]
| -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. |
| --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. |
| --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. |
| --average | Average all input placefiles together. |
| --edpl | Specify the maximum EDPL for an EDPL tree. |
Given a list of place files, --average normalizes the mass in each, then takes the average of those masses to make an appropriately averaged fat tree for those place files.
Expected Distance between Placement Locations (EDPL) values can be visualized on the tree by specifying a maximum value for the scale via the --edpl flag. The scale is represented by 0 EDPL being white, going to red for the maximum value. When EDPL is above the specified maximum, the branch is colored yellow. When there are multiple placements on a given edge, their EDPL values are combined using a weighted average, where the weights are the values of the ML weight ratio or posterior probability.