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| Resources
Articles
Web resources
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Collaborative website for the Molecular Breeding
Platform (MBP)
Generation Challenge Programme
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How the MBP can support Information Management for
Molecular Breeding
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Timeline for the development of informatics tools
for the MBP
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Using plant breeding software
Wikia Inc.
- Wageningen UR
Genetics and breeding related software which is
available for download
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Michigan State Statistical Analysis (MSTAT)
Design, management and statistical research tool
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Data Analysis for
Participatory Plant Breeding
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PBStat: A web-based statistical analysis software
for participatory plant breeding
Willy Bayuardi Suwarno, Sobir, Hajrial
Aswidinnoor, and Muhamad Syukur
The 3rd International Conference on Mathematics and
Statistics (ICoMS-3)
Bogor Agricultural University, Indonesia, August
5-6, 2008
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International Crop Information System (ICIS)
A database system that provides integrated
management of global information on genetic
resources, crop improvement and evalutation for
individual crops.
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Bioinformatics software applications from the
Scottish Crop Research Institute (SCRI)
- Flapjack
Still in development, Flapjack is a high performance
genotype visualization tool capable of handling very
large datasets., where the number of lines and/or
markers to be displayed may run into the many
thousands - this makes it a very useful tool in
genetic analysis. Flapjack allows the user to
quickly navigate around a data set, instantly
displaying any selected part of the data at any zoom
level. The tool provides a single main view of the
data, with several additional sub-views alongside,
some of which provide dynamic information depending
on where the mouse is over the main data area.
Flapjack is fully internationalized, and we
currently provide versions that run in English and
German.
- TOPALi
TOPALi provides a graphical interface to advanced
phylogenetic model selection, Bayesian analysis (BA)
and Maximum Likelihood (ML) phylogenetic tree
estimation, detection of sites under positive
selection, and recombination breakpoint location
analysis. All of TOPALi's methods can be run on
remote, high-performance computing clusters, and
many of them can be run in parallel to enhance
performance even more. TOPALi is developed by BioSS
with assistance from SBRN.
- CurlyWhirly
CurlyWhirly is a simple-to-use 3D graph viewer
suited for viewing any kind of data in three
dimensions. This includes, but is not restricted to,
output from Principal Components Analysis or
Principal Coordinate Analysis.
- Comparative Map
Viewer
Still in development, this is a graphical tool for
visualizing genetic and physical maps of genomes for
comparative purposes. Currently in prototype form,
and implemented in Java 2D and Swing, this tools
aims to let the user examine their data at a variety
of different levels of resolution, from entire maps
to individual markers, and explore syntenic
relationships between genomes.
- TetraploidMap
TetraploidMap is a graphical user interface for
calculating linkage maps for autotetraploid
populations. It is suitable for handling markers
scored on two parents and the full-sib offspring of
a cross between them. TetraploidMap handles both
codominant and dominant molecular markers, in all
possible configurations, and takes into account the
presence of null alleles in the analysis. It now
includes a routine for QTL mapping. TetraploidMap is
developed by BioSS.
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Phenom-Networks: software solutions for plant
breeding
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QU-GENE
software (The University of Queensland)
Developed to be a flexible
platform for investigation of the characteristics of
genetic systems undergoing repeated cycles of
selection and marking
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Software of Applied Genetics and Plant Breeding
(Hohenheim University)
- PLABSTAT: A
concise package to analyse plant breeding
experiments (lattices, unreplicated and multi-factor
experiments)
- PLABQTL: QTL analysis with composite interval
mapping (regression method)
Presentations
Books
Misc.
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