The post-genomic era of biological network alignment

Faisal, Fazle E; Meng, Lei; Crawford, Joseph; Milenković, Tijana

doi:10.1186/s13637-015-0022-9

EURASIP Journal on Bioinformatics and Systems Biology

Table 1 Overview of prominent network alignment approaches

From: The post-genomic era of biological network alignment

Network	Local or	Pairwise or	One-to-one or	Link to the
aligner	global?	multiple?	many-to-many?	software
PathBLAST [93]	Local	Pairwise	Many-to-many	http://www.pathblast.org
NetworkBLAST [46]	Local	Pairwise	Many-to-many	http://www.cs.tau.ac.il/~bnet/networkblast.htm
MaWISh [48]	Local	Pairwise	Many-to-many	http://compbio.case.edu/koyuturk/software/mawish
Graemlin 1.0 [47]	Local	Multiple	Many-to-many	http://graemlin.stanford.edu
NetworkBLAST-M [94]	Local	Multiple	Many-to-many	http://www.cs.tau.ac.il/~bnet/License-nbm.htm
NetAligner [54]	Local	Pairwise	Many-to-many	http://netaligner.irbbarcelona.org
AlignNemo [52]	Local	Pairwise	Many-to-many	http://www.sourceforge.net/p/alignnemo/home/Home
AlignMCL [53]	Local	Pairwise	Many-to-many	http://sites.google.com/site/alignmcl
IsoRank [55]	Global	Pairwise	One-to-one	http://groups.csail.mit.edu/cb/mna
IsoRankN [59]	Global	Multiple	Many-to-many	http://groups.csail.mit.edu/cb/mna
GRAAL [38]	Global	Pairwise	One-to-one	http://bio-nets.doc.ic.ac.uk/GRAAL_suppl_inf
H-GRAAL [39]	Global	Pairwise	One-to-one	http://www.nd.edu/~cone/software_data.html
MI-GRAAL [40]	Global	Pairwise	One-to-one	http://bio-nets.doc.ic.ac.uk/MI-GRAAL
GHOST [60]	Global	Pairwise	One-to-one	http://www.cs.cmu.edu/~ckingsf/software/ghost
SPINAL [67]	Global	Pairwise	One-to-one	http://code.google.com/p/spinal
SMETANA [74]	Global	Multiple	Many-to-many	http://www.ece.tamu.edu/~bjyoon/SMETANA
BEAMS [75]	Global	Multiple	Many-to-many	http://webprs.khas.edu.tr/~cesim/BEAMS.tar.gz
NetCoffee [76]	Global	Multiple	Many-to-many	http://code.google.com/p/netcoffee
FUSE [78]	Global	Multiple	One-to-one	Available upon e-mail request until formally published
NETAL [68]	Global	Pairwise	One-to-one	http://bioinf.modares.ac.ir/software/netal
GraphM [58]	Global	Pairwise	One-to-one	http://cbio.ensmp.fr/~mzaslavskiy/pwp_projects.html
NATALIE 2.0 [64]	Global	Pairwise	One-to-one	http://www.mi.fu-berlin.de/w/LiSA/Natalie
GEDEVO-M [77]	Global	Multiple	One-to-one	http://gedevo.mpi-inf.mpg.de/multiple-network-alignment
MAGNA [69]	Global	Pairwise	One-to-one	http://www.nd.edu/~cone/MAGNA
WAVE [73]	Global	Pairwise	One-to-one	Available upon e-mail request until formally published
GREAT [72]	Global	Pairwise	One-to-one	Available upon e-mail request until formally published
PINALOG [65]	Global	Pairwise	One-to-one	http://www.sbg.bio.ic.ac.uk/~pinalog

In the table, there are eight local and 19 global network aligners. Of the eight local aligners, six are pairwise and two are multiple, and all eight are many-to-many. Of the 19 global aligners, 13 are pairwise and six are multiple, and 15 are one-to-one and four are many-to-many. All global pairwise approaches are one-to-one, while global multiple approaches are either one-to-one or many-to-many

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