Softwares

Here we list the softwares developed and under development by the Statiscal-Genetics Laboratory and partners.

OneMap

Software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and backcrosses. To install, we recommend the under development (and constantly upgraded) version from github:

• www.github.com/augusto-garcia/onemap

Otherwise, you can install the stable version:

• https://cran.r-project.org/web/packages/onemap/index.html

The original article can be found at:

• Margarido, G. R. A., A. P. Souza, and A. A. F. Garcia. “OneMap: software for genetic mapping in outcrossing species.” Hereditas 144.3 (2007): 78-79.

SuperMASSA

It is a graphical Bayesian inference tool for genotyping polyploid compatible with any quantitative genotyping methods. It was mainly developed by Oliver Serang as visiting scientist in the Lab. A suitable pipeline adapted for many markers will be released soon. It can be found at:

• http://statgen.esalq.usp.br/SuperMASSA/

The original article can be found at:

• Serang, Oliver, Marcelo Mollinari, and Antonio Augusto Franco Garcia. “Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids.” PLoS One 7.2 (2012): e30906.

AGHMatrix

It is an R package to compute relationship matrices for diploid and autopolyploid species. It handles pedigree and molecular data with dosage. It has been developed in collaboration with Bluberry Breeding & Genomic Lab at University of Florida. It can be found at:

• https://github.com/prmunoz/AGHmatrix

The original article can be found at:

• Amadeu, Rodrigo R., et al. “AGHmatrix: R Package to Construct Relationship Matrices for Autotetraploid and Diploid Species: A Blueberry Example.” The plant genome (2016).

fullsibQTL

Software for QTL mapping in outcrossing species using composite interval mapping. It is under development and will be released soon. Based on Gazaffi et. al 2014.