##Program to check if a tree realizes a matrix

A sample call follows

./check_tree -m test/a.matrix -p test/a.tree

Options:

• ```-m``` the file containing the matrix
  

• ```-p``` the file containing the phylogeny in pseudo-Newick
  

format

• ```-d``` to output lots of debugging information
  

If the phylogeny realizes the matrix then the program produces no output. Otherwise gives a list of species of the matrix that are not realized by the tree.

A sample call follows

./tree -m test/a.matrix

Produces the phylogeny (in pseudo-Newick format) that realizes the matrix. The program assumes that the input matrix has a phylogeny, the output is undefined if the matrix has no phylogeny.

Options:

• ```-m``` the file containing the matrix
  

• ```-p``` if the input is an extended matrix, alternating
  

positive and negative characters. This case is suitable to generate a persistent phylogeny. If this option is missing, it computes a perfect phylogeny.

• ```-d``` to output lots of debugging information
  

A sample call follows

./generate-persistent-phylogeny -p ~/lib/msdir/ms -n 20 -m 30 -r 10

Generates some random instances, all admitting a persistent phylogeny

Options:

• ```-m``` the number of characters
  

• ```-n``` the number of species
  

• ```-r``` the number of instances to generate
  

• ```-p``` the path to the ms executable that is used to actually
  produce the matrix.