GenoMatrix

Developed by:
Alireza Nazarian and Salvador Gezan
School of Forest Resources & Conservation
University of Florida

GenoMatrix software is a user-friendly tool developed to facilitate the implementation of G-BLUP and P-BLUP analyses on complex traits. It consists of the following modules which collectively generate a workflow to perform data quality control, to obtain the pedigree-based and genomic additive, dominance and epistatic relationship matrices and their inverses, to merge and compare them with each other, and finally to predict unobserved (or yet-to-be observed) phenotypes in the context of reduced animal model (RAM) analyses.

Modules

  • Pedigree Sort Module (PSM): sorts the pedigree file, containing parentage information, by correcting duplicated or missing entries so that no progeny appears after its parents.
  • Pedigree-based Relationship Matrix Calculation Module (PRM): generates the pedigree-based additive and dominance relationship matrices based on the expected proportions of identical-by-descent (IBD) loci across genome of any pair of individuals.
  • Quality Control Module (QCM): refines the input genotyping data based on multiple user-specified quality control measures.
  • Genomic Relationship Matrix Calculation Module (GRM): generates the genomic additive and dominance relationship matrices based on the observed IBD proportions across the genotyped loci of any pair of individuals.
  • Epistatic Matrix Calculation Module (EMM): generates the pedigree-based and genomic epistatic relationship matrices.
  • Inverse Matrix Calculation Module (IMM): generates the inverse of relationship matrices and deals with matrix singularity issue.
  • Pedigree Manipulation Module (PMM): aligns, merges and compares the pedigree-based and genomic relationship matrices, or adjusts the genomic relationship matrices.
  • Genetic Prediction Module (GPM): predicts unobserved responses given availability of the response values for a portion of subjects under consideration and a relationship matrix for the entire set of subjects (i.e. with and without response values).

Availability

GenoMatrix is distributed as a Windows 64bit executable. It is available for data analysis to research community and commercial users free of charge. However, users are required to properly cite the copyright holders. The downloadable package contains the compiled application, the user guide and a set of simulated datasets for testing the package functionality.

Download GenoMatrix

Data files

The following additional data files are available for download:

Prerequisites

Users need to download the compatible MATLAB Runtime [i.e. MCR version 9 (R2015b) for Windows 64-bit] from the MathWorks website and follow the installation wizard to install it if:

  • MATLAB is not installed on their machines, or
  • The version of installed MATLAB MCR on their machines is anything except 9 (R2015b)

Contact Information

Should you have any questions, concerns or comments regarding GenoMatrix, please do not hesitate to contact us at: anazarian@ufl.edu or sgezan@ufl.edu.