Journals
Publish with us
Publishing partnerships
About us
Blog
The Scientific World Journal
Journal overview
For authors
For reviewers
For editors
Table of Contents
Special Issues
The Scientific World Journal
/
2013
/
Article
/
Tab 1
/
Review Article
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
]
MST
MAP
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/
ā
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
]