Table 1.

Comparison of related tools. We compare six publicly available tools on the basis of five criteria

	Features
Tools	Alphabet	Input format	Comparison	Clustering	Extensible
seqLogo	DNA	matrix	uniform	-	-
iceLogo	DNA/RNA, proteins	sequences	average	-	-
MotifStack	any	matrix	uniform	hclust	-
STAMP	DNA	sequences, matrix	uniform	UPGMA/SOTA	-
Two Sample Logo	DNA/RNA, proteins	sequences	position-specific	-	-
DiffLogo	any	sequences, matrix	position-specific	hclust, optimal leaf ordering	✓

In the first and second column, we examine the kind of supported input, in the third and forth column we examine the mode of action, and in the fifth column we examine whether the tool is extensible. For the criterion “alphabets” we summarize the supported biopolymers out of DNA, RNA, and proteins or arbitrary alphabets in case of “any”. For the criterion “input format” we discriminate a set of “sequences” versus “matrix”, which addresses at least one out of the formats position weight matrix (PWM), position frequency matrix (PFM), and position count matrix (PCM). For the criterion “comparison” we characterize the kind of distribution that is used for motif comparison (“uniform” is the uniform distribution, “average” is the average base distribution in a set of sequences, and “position-specific” is a position-specific distribution). For the criterion “clustering” we point out whether there is a clustering of motifs and which cluster-algorithm is used. For the criterion “extensible” we note whether the tool is extensible by the user