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Molecular breeding software tools

Breeding informatics

Software to visualize and analyse data for molecular breeding applications.

Entries in collection

EiB Galaxy instance
Cloud hosted tools from EiB, HTPG and GOBII on the Galaxy Project service.
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CGIAR Excellence in Breeding Platform
Biodiversity analysis with R (BIO-R)
R programs for biodiversity analysis of molecular data.
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Ángela Pacheco, Gregorio Alvarado, Francisco Rodríguez, Juan Burgueño
Bayesian Generalized Linear Regression in R (BGLRR)
Software to simplify the selection of input files and parameters to perform bayesian generalized linear regression using R
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Francisco Rodríguez, Paulino Pérez, Gustavo de los Campos, Gregorio Alvarado, Ángela Pacheco, José Crossa, Juan Burgueño
Spatial Multi-Environment Trial Analysis with R (Spatial META-R)
Software to simplify the selection of input files and parameters to perform spatial multi-environment trial analysis using R and ASReml
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Francisco Rodríguez, Gregorio Alvarado, Ángela Pacheco, José Crossa, Juan Burgueño
Multi Environment Trail Analysis with R (META-R)
META-R is a set of R programs that perform statistical analyses to calculate BLUEs, BLUPs, and genetic correlations for breeding trials.
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Gregorio Alvarado, Marco López, Mateo Vargas, Ángela Pacheco, Francisco Rodríguez, Juan Burgueño, José Crossa
Flapjack
Multi-platform tool for interactive visualization of high-throughput genotype data, allowing for rapid navigation and comparisons between lines, markers and chromosomes and visualization around QTL features and characterization data.
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Information & Computational Sciences, The James Hutton Institute
Helium
Multi-platform pedigree visualization tool with phenotype display.
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Paul Shaw, Jessie Kennedy, Martin Graham, James Hutton Institute, Edinburgh University