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| alignPoly | Align various types of coefficient matrices |
| allTrees | Calculate all full unordered m-ary trees up to n tips |
| plotExtremeTrees | Plot the min/max distance trees from a target tree |
| polyDist | Calculates the distance between coefficient matrices |
| polyToDistMat | Calculates the distance matrix from a list coefficient matrices |
| treeDist | Calculates the distance between trees |
| treeJuliaSet | Plots a Julia Set for a tree |
| treeToDistMat | Calculates the distance matrix from a list of phylo objects |
| treeToPoly | Convert trees to coefficient matrices |
| wedge | Performs the wedge operation |