# pmlpca¶

pmlpca performs poor-man’s length principal components.

```
usage: pmlpca [options] placefiles
```

## Options¶

--out-dir |
Specify the directory to write files to. |

--prefix |
Specify a string to be prepended to filenames. Required. |

--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. |

--gray-black |
Use gray/black in place of red/blue to signify the sign of the coefficient for that edge. |

--min-width |
Specify the minimum width for a branch to be colored and thickened. Default is 1. |

--write-n |
The number of principal coordinates to calculate (default is 5). |

--som |
The number of dimensions to rotate for support overlap minimization(default is 0; options are 0, 2, 3). |

--scale |
Scale variances to one before performing principal components. |

--symmv |
Use a complete eigendecomposition rather than power iteration. |

--raw-eval |
Output the raw eigenvalue rather than the fraction of variance. |

--kappa |
Specify the exponent for scaling between weighted and unweighted splitification. default: 1 |

--rep-edges |
Cluster neighboring edges that have splitified euclidean distance less than the argument. |

--epsilon |
The epsilon to use to determine if a split matrix’s column is constant for filtering. default: 1e-05 |