Table 1.

Summary of algorithms for comparison

Algorithm	BLAST data	Algorithm parameters	Weights	One-to-one	Enforced coverage	Type
AlignMCL	-log2 (e-value) inter-network		Yes	No	No	Local
AlignNemo	e-values inter-network		Yes	No	No	Local
CUFID	-log2 (e-value) inter-network		Yes	Yes	No	Global
HubAlign	-log2 (e-value) inter-network		No	Yes	Yes	Global
IsoRankN	-log2 (e-value) intra & inter-network	-K 10 –thresh 1e–5 –alpha 0.7 –maxveclen 2000000	No	No	No	Global
MAGNA++	-log2 (e-value) inter-network	-p 15000 -n 2000 -a 0.5 -t 4 -m S3	No	Yes	Yes	Global
MI-GRAAL	-log2 (e-value) inter-network	-p 19	No	Yes	Yes	Global
NETAL	-log2 (e-value) intra & inter-network	-b 0.5 -c 0.5	No	Yes	No	Global
NetCoffee	e-values intra & inter-network		No	Yes	No	Global
NetworkBLAST	e-values inter-network	beta 0.9; blast_th 1e–30; true_factor0 0.5; true_factor1 0.5	Yes	No	No	Local
PINALOG	-log2 (e-value) inter-network		No	Yes	No	Local
SANA	-log2 (e-value) inter-network	-s3 0.5 -sequence 0.5	No	Yes	Yes	Global
SMETANA	-log2 (e-value) inter-network		Yes	No	No	Global
WAVE	-log2 (e-value) inter-network		No	Yes	Yes	Global
PrimAlign-Seq	e-values inter-network		No	No	No	Global
PrimAlign-Topo	unweighted inter-network		No	No	No	Global
PrimAlign	-log2 (e-value) inter-network		Yes	No	No	Global

Note: Enforced coverage means that all proteins from the smaller network need to be aligned.