Table 1.

Comparison of existing state-of-the-art computational toolkits for feature engineering, extraction, calculation, analysis and visualization. Tools are sorted chronologically

Tools	Coverage of different molecule types					Performs feature analysis	Performs data visualization	Available interfaces			Ref.
	DNAs	RNAs	Protein sequences	Ligands	Protein structures			Web server	CLI stand-alone	GUI stand-alone
PIC	×	×	×	×	√	×	√	√	×	×	(46)
PseAAC	×	×	√ (3)	×	×	×	×	√	×	×	(12)
PROFEAT	×	×	√ (11)	√ (1)	×	×	×	√	×	×	(13)
PseAAC-Builder	×	×	√ (3)	×	×	×	×	×	√	√	(14)
PyDPI	×	×	√ (14)	√ (13)	×	×	×	×	√	×	(15)
ChemoPy	×	×	×	√ (19)	×	×	×	×	√	×	(16)
Propy	×	×	√ (13)	×	×	×	×	×	√	×	(17)
PseAAC-General	×	×	√ (13)	×	×	×	×	×	√	×	(19)
Rcpi	×	×	√ (10)	√ (8)	×	×	×	×	√	×	(20)
Protr/ProtrWeb	×	×	√ (22)	×	×	×	×	×	√	×	(22)
BioTriangle	√(14)	√(14)	√(14)	√(18)	×	×	×	√	×	×	(23)
PDBparam	×	×	×	×	√(4)	×	×	√	×	×	(47)
repRNA	×	√ (11)	×	×	×	×	×	√	×	×	(24)
PseKRAAC	×	×	√ (16)	×	×	×	×	√	×	×	(26)
iFeature	×	×	√ (53)	×	×	√(10)	√(2)	√	√	×	(27)
PyFeat	√(13)	√ (13)	√(9)	×	×	×	×	×	√	×	(28)
Seq2Feature	√(1)	√(1)	√ (4)	×	×	×	×	√	×	×	(29)
BioSeq-Analysis2.0*	√(36)	√(27)	√(53)	×	×	√(2)	√(1)	√	√	×	(32)
PFeature*	×	×	√	×	√	×	×	√	√	×	(33)
iLearn*	√(26)	√(18)	√(53)	×	×	√(15)	√(3)	√	√	×	(34)
iLearnPlus*	√(46)	√(35)	√(66)	×	×	√(20)	√(7)	√	×	√	(5)
MathFeature	√(30)	√(30)	√(12)	×	×	×	×	×	√	√	(31)
iFeatureOmega	√(49)	√(37)	√(71)	√(18)	√(14)	√(15)	√(9)	√	√	√	-

Note: *the tool is a machine-learning platform. ‘X’ means that the function is unavailable. Numbers in the brackets denote the numbers of different feature sets, or analysis/visualization options.