Usage:
-A: (usage -A seqFileName): Ancestral sequences file name;
-b: (usage -b): If this flag is on, branch length for the input tree are first
				ML optimized, using the specified stochastic process.
-d: Specified the Markov model
	(usage -dd): Set amino-acid model to be based on the Dayhoff matrix.  
	(usage -dj): Set amino-acid model to be based on the JTT matrix.  
	(usage -dr): Set amino-acid model to be based on the REV matrix.  
	(usage -dA): Set amino-acid model to be based on the Jokes and Cantor.  
	(usage -dn): Set nucletide model to be based on the Jokes and Cantor.  
	default: modelName=JTT (Amino-acids).

-F  (usage -F logFileName): set the log file, for debugging and run time information.
	default: log.txt
-g  (usage -g) Gaps are removed from the alignment

-m: Determine the bound used:
	(usage -ms) Using bound based on maximum; (see paper)
	(usage -mm) Using bound based on sigma; (see paper)
	(usage -mb) Using bound based on both; (see paper)
	default: Bound Method=both;
-o	(usage -o treeFileName): Print the tree used. If branch length optimization was performed,
	printing the tree after branch lengths optimization.
	default: tree is printed to the cout stream (terminal).
-p	(usage -p floatingPointNumber): Input the gamma distribution parameter that models the among-site-rate-variation.
					   if  the parameter is zero, the parameter is estimated from the data.
					   note: this may take a lot of time, since it is ML estimation.
					   default: the default gamma parameter is 1.0
-P   (usage -P integer_number): The number of descrete gamma categories used to approximate the gamma distribution.
	 default: 4
-Q	 The sequences file format:
	 (usage -Qc): clustal format 
	 (usage -Qf): fasta format 
	 (usage -Qm): mase format 
	 (usage -Qp): phylip format 
	 default: clustal format
-r	 (usage -r) Sets the distribution to be gamma shaped
	 default: homogenous model.
-R:  (usage -R reportFileName) sets a report file, to which some statistics of the algorithm
	 are printed (time, number of nodes visited, etc...);
	 default: The report is not active
-s:  (usage -s seqFileName) sets the sequence file name.
	 default: This argument must be given!
-t:  (usage -s treeFileName) sets the tree file name.
	 default: This argument must be given!

Advances options:
-a: (usage -a floatingPointNumber): Determine a marginal probability threshold. 
	In each step of the argorithm the order of amino-acid replacements
	are recomputed according to the marginal probabilities. After each 
	character assignment these probability change. Recomputing these marginal 
	takes time, but it is possible that according to the new marginals, one can
	cut bigger parts of the search tree. Default value: 0.9

-C: (usage -C): Sequence are input from Cin. 
-v: (usage -v integerNumber) set the amound of verbus information to the log file;