Changes on version ...


- file 'covarion' added. It is an adjustment of file 'evolve' to simulate the
hidden process evolution (ON/OFF states and times spent on 'ON' along the branches).

- files 'tree' and 'treefile' modified to add new features to the 'TNode' structure. 
These 2 new features are hiddenStates and effectiveLength0.

- file 'evolve' modified to adjust for the covarion case:
	in function 'EvolveNode'
	in functions 'Write...Format'

- file 'seq-gen' modified: 
	Option -v added in function 'PrintUsage',
	'ReadParams' modified accordingly,
	in 'main', the call to 'EvolveHiddenStates' is added.