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MADroot

Efficient implementation of the MAD method for inferring the location of the root in a large phylogeny.

The MAD method for rooting a phylogeny was first described in

Tria, F. D. K., Landan, G., and Dagan, T. (2017). Phylogenetic rooting using minimal ancestor deviation. Nature Ecology and Evolution, 1, 0193.

This is an implementation of the O(n^2) time and linear space algorithm outlined in

Bryant, David, and Michael Charleston. "MAD roots for large trees." arXiv preprint arXiv:1811.03174 (2018).

Contents

  • 'madRoot.cpp' Code for the MAD root procedure, and for the simulations performed in the paper.
  • 'madRoot.R' An R script giving an (inline) version of the madRoot algorithm
  • 'Makefile' Make file.
  • 'smallExample.txt' Small (four taxa) example
  • 'largeExample.txt' Large (3082 taxa) example Note that this code makes use of the PhyLib library (here included as a submodule).

Downloading

In a terminal window, execute git clone --recursive git@github.com:davidjamesbryant/MADroot.git

Building

madRoot executable

Change to the directory 'MADroot'. Make sure that 'madRoot.cpp', 'Makefile' and the 'Phylib' directory are in the same folder, then type 'make'.

To run the algorithm on the tree in the tree file call madRoot

To repeat the simulation/benchmark performed in Bryant and Charleston, run madRoot -SIM

madRoot (inline) R.

in R, make MADroot your working directory. Install the packages 'Rcpp' and 'inline'. When you execute 'madRoot'R' it will create a new function in R called 'madRoot'. You can run 'madRoot' using madRoot(treeString) where treeString is a string (character vector) containing one or more trees in NEWICK notation, separated by semicolons.