I know there is probably no "best" option, but I am looking for opinions on software to manage a plant breeding program. It would be primarily traditional breeding for the time being.
So far I have been looking into PRISM, Doraine, or Agronomix, but nothing is set in stone. Any thoughts or feedback out there?
Hello Jones,
Kindly visit the IRRI website (http://bbi.irri.org/products). They have some interesting software and statistical packages that may be of interest to you. PBTools (Plant Breeding Tools) could be a good package to start with.
Best,
Try GENES software. It is useful for analyzing and processing phenotypic and molecular data using different biometric models.
But genes software is mostly in Portuguese. Difficult to use. Most of the examples are in Portuguese. I think it is not user friendly
If they examples and input method easily, then Genes software must be a useful one
SAS can be considered as a useful and power tool in plant breeding experiments.
R can also be used with agricolae, plant breeding packages in most of the general plant breeding experiments and so many
packagess available for specific experiments.
Please, check this site: https://www.e-brida.com/plant-breeding-software-e-brida/
The most comprehensive software is Genovix by Agronomix https://www.agronomix.com. It has a mobile app (android, iOS and Windows) for data collection and uses R for analyses. It does stats and graphical output. It's used in some universities and by the Plant Breeding Academy.
They also have a very interesting blog: https://plantbreedingsoftware.guru/
You could as well check DeltaGen https://deltagen.agresearch.co.nz/app/deltagen.
Santoshkumar B Pujer Do you have access to windowstat? how we can get one for ourselves??
As a beginner one can use drop down or menu based softwares like indostat, XLstat or SPSS for simple experimental analyses. Specifically for plant breeding experiments, GENstat is powerful menu based software. Apart from that, PBTools from IRRI can also be used without any difficulty. For multiplication experiments, CIMMYT has some open softwares which works in R background. However, breeders can use SAS or R softwares for any analyses with appropriate packages, many tutorials/online codes also available.
The key should be what you wish to analyse, no software will be providing all the analysis, unless you are either working with SAS and or R. While SAS is a licensed one, R comes free however will require certain level of expertise to finally find the scripts or modify them on your own for an analysis. JMP, if one can find it free is also good especially for graphical analysis. If analysis is limited excel it self can help one a lot especially if one opts for adds-in in data analysis. most of the functions in excel remain unexplored by us. SPSS, its old versions are free to download and its quite easy to operate as well and its demo video's and help are available online. PBTools as mentioned above as well, is good but it has limited applications of dealing with experimental designs. The IASRI webpage provides lots of information on designs and layouts and also some online analysis as well. Most easy for breeders or agronomist can be OPSTAT (http://14.139.232.166/opstat) its is online analysis and covers most of the analysis that will be required on day to day busy, very easy to operate, the data feed format is given for every analysis and it goes by choosing the given options as menu by menu, also the output is easy and can imported to excel and is report ready as well without much changes. Another free software that can be very usefull is PAST 3. Its a simple excel based programe and very good and easy for graphs, correlations and multivariate analysis especially PCA and clustering
Breeding management System. Its been developed in collaboration with CIMMYT. It can work independently as well as can be linked through net. Free, unlike others just requires registration.
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