Breeding informatics

EiB Galaxy instance

Galaxy is an open-source application to enable researchers without informatics expertise to perform computational analyses through the web. A user interacts with Galaxy through the web by uploading and analyzing the data. Galaxy interacts with underlying computational infrastructure (servers that run the analyses and disks that store the data) without exposing it to the user.

Sample Tracker

Sample Tracker is a web-based application developed by the International Maize and Wheat Improvement Center (CIMMYT) to facilitate the workflow and sample identity assignation and tracing around DNA sampling.

Sample tracker provides interfaces to load, generate and query scientist and project information, sample information, genotyping provider requisite plate layouts, plate layouts for lab implementation of DNA extraction, QC metric capture, DNA storage locations, sample file generation and shipping management.


SNPviewer is a tool that enables genotyping data to be viewed as a cluster plot, but that does not include data analysis or reporting functionality.

Opening genotyping service project results in SNPviewer will allow you to view the genotyping clusters plate by plate. Genotyping calls cannot be changed within SNPviewer; if you need to be able to edit the calls then you will require our KlusterCaller software.



Coordinate replaces our previous DNA Plate App and Seed Tray App with a unified data collection app. Coordinate is based on defining templates and then collecting data in grids created from those templates. Two templates are included by default: Seed Tray and DNA Plate.


Verify is a simple app for importing and managing a list of entries. Utilizing an internal or external barcode scanner, Verify can identify individuals in the list, keep track of how many times they've been scanned, and order in which the items are scanned are correct.

In its simplest form, Verify is integral for viewing data associated with a given entry, making it very useful for sample tracking and management. Sample files are provided with the installation to demonstrate the utility of Verify in research programs.


CassavaBase offers access to data and tools for breeders and researchers, including genomic selection algorithms and analysis capacity, a cassava genome browser, cassava ontology tools, phenotyping tools, and social networking.

Examples of activities supported by CassavaBase:

The Breeding Management System (BMS)

The Breeding Management System (BMS) is a program that helps manage your breeding data across all phases of the crop improvement cycle, from program planning to decision making.

It lets you manage trials, nurseries and seed inventory; run statistical analyses; and support breeding decisions through the gradual integration of genetic markers.

The BMS suite of tools supports multiple breeding strategies:

Biodiversity analysis with R (BIO-R)

Biodiversity analysis with R (BIO-R) is a set of R programs that do biodiversity analysis of molecular data, in order to calculate heterozygosity, diversity among and within groups, shannon index, number of effective allele, percent of polymorphic loci, Rogers distance, Nei distance, cluster analysis and multidimensional scaling 2D plot and 3D plot

You can include external groups for colored dendogram or MDS plots, and additionally obtain a Core Subset using molecular data and also phenotypic, geographical and any source of data.

Bayesian Generalized Linear Regression in R (BGLRR)

Bayesian Generalized Linear Regression in R (BGLRR) is a software to simplify the selection of input files and parameters to perform Bayesian Generalized Linear Regression using R (statistical software).

BGLR provides predictions, genome-wide association study (GWAS) analysis and analysis of reaction norm models. It allows the inclusion of markers information, relationship matrix (pedigree), environmental covariables, and other variables as fixed or random effects.

Spatial Multi-Environment Trial Analysis with R (Spatial META-R)

Spatial META-R is a software to simplify the selection of input files and parameters to perform spatial multi-environment trial analysis using R (statistical software) and ASReml v1.0 free version.

Spatial META-R provides the calculus of best linear unbiased estimates (BLUEs), best linear unbiased predictions (BLUPs), genetic correlations among locations and genetic correlations between variables, and broad-sense heritability. Analyses may be performed by location, across management conditions or across all locations.