9/20/2006:

An initial attempt to put together the program.

Files include:

main.c - the main program
bme.c - BME functions
gme.c - GME functions
NNI.c - FastNNI functions
bNNI.c - BNNI functions
inputs.c - for inputting matrices
graph.c - basic functions for tree creation
newick.c - functions for inputting and outputting trees in Newick format
heap.c - routines for handling heap for NNI and BNNI
BIONJ.C - NJ and BIONJ functions
traverse.c - functions to move through tree
interface_options.c - PHYLIP like interface
interface_utilities.c - useful function for PHYLIP like interface
interface_free.c - functions to free memory allocated for PHYLIP like interface

The program can be used through the PHYLIP like interface. In that case, just
run it with no parameter.

With the command line interface, the program takes six different flags:
Usage: fastme -ibnstw
-i filename of distance matrix.
-b method for building initial tree: (b)alanced_GME (default), (O)LS_GME,
   B(I)ONJ or (N)J.
-n number of trees/matrices input (default = 1).
-s specify type of tree swapping (NNIs): (b)alanced (default), (O)LS, or (n)one.
-t (optional) filename of starting tree topology.
-w (b)alanced or (O)LS weights. (n)one is available only with NJ or BIONJ tree
   building method.
-help to get this message.

FastME creates two output files:
- The output tree: {matrix_filename}_tree.txt
- The statistical informations: {matrix_filename}_stat.txt
