Application of computational methods in genetic study of inflammatory bowel disease

Table 1 Commonly used publically available software for each step in genomic studies

Analysis	Software	URL	Ref.
GWAS	PLINK	http://pngu.mgh.harvard.edu/~purcell/plink/	[7]
	EMMAX	http://genetics.cs.ucla.edu/emmax/	[10]
	FaST	http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/Fastlmm/	[13]
	GEMMA	http://www.xzlab.org/software.html	[14]
Imputation	SHAPEIT (pre-phasing)	https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html	[20]
	IMPUTE2 (pre-phasing and imputation)	https://mathgen.stats.ox.ac.uk/impute/impute_v2.html	[17]
	MACH (pre-phasing and imputation)	http://csg.sph.umich.edu//abecasis/MACH/tour/imputation.html	[18]
	fastPHASE (pre-phasing and imputation)	https://els.comotion.uw.edu/express_license_technologies/fastphase	[16]
	BEAGLE (pre-phasing and imputation)	http://faculty.washington.edu/browning/beagle/beagle.html	[19]
	SNPTEST (association testing)	https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest.html	[22]
Meta-analysis	METAL	http://csg.sph.umich.edu//abecasis/Metal/	[27]
	META	https://mathgen.stats.ox.ac.uk/genetics_software/meta/meta.html	[22]
	MetABEL	http://www.genabel.org/packages/MetABEL	[30]
	GWAMA	http://www.well.ox.ac.uk/gwama/download.shtml	[31]
	PLINK	http://pngu.mgh.harvard.edu/~purcell/plink/metaanal.shtml	[7]
Pathway analysis	GenGen	http://gengen.openbioinformatics.org/en/latest/tutorial/pathway/	[34]
	ALIGATOR	http://x004.psycm.uwcm.ac.uk/~peter/	[39]
	i-GSEA4GWAS	http://gsea4gwas.psych.ac.cn/	[40]
	GSEA-SNP	https://http://www.nr.no/en/projects/software-genomics	[41]
	DAVID	http://david.ncifcrf.gov/summary.jsp	[42]
	GeneTrail	http://genetrail.bioinf.uni-sb.de/	[43]
	WebGestalt	http://bioinfo.vanderbilt.edu/webgestalt/	[44]
Network analysis	Cytoscape	http://www.cytoscape.org/	[45]
	DAPPLE	http://www.broadinstitute.org/mpg/dapple/dappleTMP.php	[46]
	STRINGS	http://string-db.org/	[47]
	FUNCOUP	http://funcoup.sbc.su.se/search/	[48]
Gene-gene interaction	PLINK	http://pngu.mgh.harvard.edu/~purcell/plink/epi.shtml	[7]
	BOOST	http://bioinformatics.ust.hk/BOOST.html	[52]
	MDR	https://ritchielab.psu.edu/mdr-downloads	[55]
Microbiome	QIIME	http://qiime.org/	[69]
	mothur	http://www.mothur.org/wiki/Main_Page	[71]
	VAMPS	https://vamps.mbl.edu/portals/hmp/hmp.php	[72]
	PhymmBL	http://ccb.jhu.edu/software/phymmbl/index.shtml	[73]
	MEGAN5	http://ab.inf.uni-tuebingen.de/software/megan5/	[74]
	PhyIOTU	https://github.com/sharpton/PhylOTU	[75]
	MLTreeMap	http://mltreemap.org/	[76]
Pleiotropy	CPMA	http://coruscant.itmat.upenn.edu/software.html	[92]
	ASSET	http://www.bioconductor.org/packages/release/bioc/html/ASSET.html	[93]
	GPA	https://github.com/dongjunchung/GPA	[98]
	SMAT	http://www.hsph.harvard.edu/xlin/software.html	[101]