"progresive2" is the primary tool to search for conserved domains.
This creates and analyzes signals acording to Beta size windows.
Based on alignment free method by Spectrum comparison, this function
constructs a phylogenetic tree. Taking into account the most related
sequences, it fractions its corresponding signals into \beta size
windows. After window redundancy elimination, it will progressively
compare the windows with each of the remaining signals, sliding an
increase step at a time and evaluate if the comparison is valid
considering a treshold for the comparison tools score. If so, it will
tag the position of the signal where the "hit" occurred. The function input are
the sequence set {seq1;seq2...seqn,1}, the headers set {header1;
header2...headern,1} and the alpha value decided by sequence similarity,
the beta size of the windows and the increase step of the sliding window.
The output is the window sequence, the window hits and the hits position for each window.
Each column corresponds to each of the original sequences compared, within,
the cell corresponds to the windows generated, and within the values for
each variable. In Windowsequence the value will be the window sequence,
in WindowHits will be a vector with the result of each of the sliding
comparisons 1 for a hit 0 otherwise; in WindowHitPosition the value will
be the point of the signal where a hit exist (it corresponds to
Windowhits).

Function Structure

progresive2
	FFTnonfiltered
		DNAmeltingArbitrary
			EnergyPairParamArbitrary
		Signalpretreatment
	orderpointers
		orderloop
			validate
				findorder
				findpointer
			findorder
			findpointer
		whoisless
		additnow
		findpointer
		findnode
	getseqpair
	Createwindowsforprogresive
		DNAmeltingArbitrary
			EnergyPairParamArbitrary
		Signalpretreatment
		delrepeatwinincluded
	localalignmentwindows2
		DNAmeltingArbitrary
			EnergyPairParamArbitrary
		Signalpretreatment
		arfit
			arord
			arqr
		coherencia