Emerging Paradigms in Genomics-Based Crop Improvement

Table 1

List of softwares used for various analyses in molecular breeding.

Name of software	URL	Reference
Linkage map construction
MAPMAKER/EXP	http://www2.hawaii.edu/~durrell/Software/B14F5F09-6238-43DA-B95F-958D4FB709AD.html	[18]
JoinMap	http://www.kyazma.nl/index.php/mc.JoinMap	[19]
RECORD	http://www.wageningenur.nl/en/show/RECORD.htm	[20]
AntMap	http://lbm.ab.a.u-tokyo.ac.jp/~iwata/antmap/	[21]
MSTMAP	http://alumni.cs.ucr.edu/~yonghui/mstmap.html	[22]
MergeMap	http://138.23.178.42/mgmap/	[23]
MultiPoint	http://www.multiqtl.com/	[24]
Family based QTL discovery
MAPL	http://lbm.ab.a.u-tokyo.ac.jp/~ukai/	[25]
MapQTL	http://www.kyazma.nl/index.php/mc.MapQTL	[26]
PLABQTL	http://wheat.pw.usda.gov/jag/papers96/paper196/utz.html	[27]
QGene	http://www.qgene.org/qgene/index.php	[28]
BQTL	http://famprevmed.ucsd.edu/faculty/cberry/bqtl/	[29]
Map Manager QTX (QTX)	http://www.mapmanager.org/	[30]
Windows QTL Cartographer	http://statgen.ncsu.edu/qtlcart/WQTLCart.htm	[31]
MCQTL	http://carlit.toulouse.inra.fr/MCQTL/	[32]
GMM	http://www.kazusa.or.jp/GMM/	[33]
ICIM	http://wiki.cimmyt.org/confluence/display/MBP/Application+2.2.5+Tool+7.10+QTL+IciMapping	[34]
QTLNetwork	http://ibi.zju.edu.cn/software/qtlnetwork/	[35]
R/qtl	http://www.rqtl.org/	[36]
MultiQTL	http://www.multiqtl.com/	—
LD analysis (Population structure/Marker-trait association)
STRUCTURE	http://pritch.bsd.uchicago.edu/software/structure2_2.html	[37]
EIGENSTRAT	http://www.mybiosoftware.com/population-genetics/1309	[38]
GeneRecon	http://www.daimi.au.dk/~mailund/GeneRecon/	[39]
GENOMIZER	http://www.ikmb.uni-kiel.de/genomizer/	[40]
BMapBuilder	http://bios.ugr.es/BMapBuilder/	[41]
CaTS	http://www.sph.umich.edu/csg/abecasis/CaTS/	[42]
MIDAS	http://www.genes.org.uk/software/midas	[43]
TASSEL	http://sourceforge.net/projects/tassel/	[44]
InStruct	http://cbsuapps.tc.cornell.edu/InStruct.aspx	[45]
PLINK	http://pngu.mgh.harvard.edu/~purcell/plink/	[46]
GenAMap	http://cogito-b.ml.cmu.edu/genamap/	[47]
GWAPP	http://gwas.gmi.oeaw.ac.at/#!home	[48]
ALDER	http://groups.csail.mit.edu/cb/alder/	[49]
MAGIC analysis
R-version of HAPPY	http://www.well.ox.ac.uk/happy/happyR.shtml	[50]
mpMap	http://www.mybiosoftware.com/population-genetics/6437	[51]
Genomic selection
R-Package for GS	http://www.r-project.org	[52]