squash performs squash clustering.
usage: squash [options] placefiles
| --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. |
| --seed | Set the random seed, an integer > 0. Default is 1. |
| --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. |
| --out-dir | Specify the directory to write files to. |
| --prefix | Specify a string to be prepended to filenames. |
| -p | Exponent for KR integration, i.e. value of p in Z_p. Default 1. |
| --normalize | Divide KR by a given value. Legal arguments are “tree-length”. |
| --bootstrap | the number of bootstrap replicates to run |
| -j | The number of processes to spawn to do bootstrapping. default: 2 |
| --tax-cluster | Perform taxonomic clustering rather than phylogenetic.Specify “unit” or “inv” for the two different modes. |
| --pre-round | Apply rounding with 3 sig figs and cutoff 0.01 to each placerun before clustering |
| --unitize | Unitize masses after bootstrap resampling |
Perform squash clustering.
Bootstrapping is performed by resampling directly on placements. Note that the bootstrap values for clustering are calculated in a rooted way. That means that you may observe different bootstrap values on either side of the root, especially if a whole clade from one side of the root likes to flip to a location distal to the clade on the other side of the root.