hakmer Files

Installation has been checked on Mac OSX and Linux machines.
By and large it works simply by executing the included
bare-bones makefile. 

From within the 'dist' directory:

	cd src
	make

There may be a number of warnings, which can be ignored,
but when finished the code for hakmer should be present
in the src directory.

Type

	chmod +x hakmer

and to see the help listing for the code type

	./hakmer -h

I have included a small sample data set called 'Fabaceae18.fa'
containing 18 angiosperm plastid genomes. You can test the 
program by getting out to the 'dist' directory and typing

	src/hakmer -f Fabaceae18.fa -s super.nex

This will create a supermatrix with some 121,000 sites for 18
species in the angiosperm family Fabaceae. The program writes
a nexus file for the matrix and a file with charsets (in nexus
format), which indicates the positions (within the data matrix
--not the original sequences) of the k-mers proper, excluding 
their flanking regions. This may be of interest if you want to
exclude the k-mers and just do inference with the flanks.