################## Content ##################

# Build procedure
# Getting started
# Executables
### triplet_distance
### quartet_distance
### all_pairs_triplet_distance
### all_pairt_quartet_distance
# Newick format
# Contact

############### Build procedure: ###############

To build and install the library, unzip the directory and execute the
following commands in a terminal:

$ cd <path to library>/tq-1.0.1/
tqDist-1.0.0 $ cmake .
tqDist-1.0.0 $ make
tqDist-1.0.0 $ make test
tqDist-1.0.0 $ make install

################ Executables ###################

## triplet_distance

Usage: bin/triplet_dist <filename1> <filename2>

Where <filename1> and <filename2> point to two files each containing one
tree in Newick format. In both trees all leaves should be labeled and the
two trees should have the same set of leaf labels.
The triplet distance between the two trees will be printed to stdout.

## quartet_distance

Usage: bin/quartet_dist <filename1> <filename2>

Where: <filename1> and <filename2> point to two files each containing
one tree in Newick format. In both trees all leaves should be labeled
and the two trees should have the same set of leaf labels.
The quartet distance between the two trees will be printed to stdout.

## all_pairs_triplet_distance

Usage: bin/all_pairs_triplet_dist <input filename> [output filename]

Where:
	<input filename> is the name of a file containing multiple trees in
	Newick format. Each tree should be on a seperate line. In each tree
	all leaves should be labeled and all trees should have the same set
	of leaf labels.
	If [output filename] is specified the output is written to the file
	pointed to (if the file already exists the current content is deleted
	first), otherwise the output is written to stdout.
	The output is a lower triangular matrix in which the i, j'th entry
	is the pairwise triplet distance between the tree on line i and the
	tree on line j in <input filename>.

## all_pairs_quartet_distance

Usage: bin/all_pairs_quartet_dist <input filename> [output filename]

Where:
	<input filename> is the name of a file containing multiple trees in
	Newick format. Each tree should be on a seperate line. In each tree
	all leaves should be labeled and all trees should have the same set
	of leaf labels.
	If [output filename] is specified the output is written to the file
	pointed to (if the file already exists the current content is deleted
	first), otherwise the output is written to stdout.
	The output is a lower triangular matrix in which the i, j'th entry
	is the pairwise quartet distance between the tree on line i and the
	tree on line j in <input filename>.

################ Newick format: ################

For details on how to encode trees in Newick format see

    http://en.wikipedia.org/wiki/Newick_format

################## Contact #####################

If you encounter any problems or have questions about using this
software, please contact

	  Christian N. S. Pedersen : cstorm@birc.au.dk.
