Data from multi environment agronomic trials, which are often 
  carried out by plant breeders, can be analyzed with the tools offered by this 
  package such as the Additive Main effects and Multiplicative Interaction model 
  or 'AMMI' ('Gauch' 1992, ISBN:9780444892409) 
  and the Site Regression model or 'SREG' ('Cornelius' 1996, 
  <doi:10.1201/9780367802226>). Since these methods present a poor performance 
  under the presence of outliers and missing values, this package includes 
  robust versions of the 'AMMI' model ('Rodrigues' 2016, 
  <doi:10.1093/bioinformatics/btv533>), and also imputation techniques 
  specifically developed for this kind of data ('Arciniegas-Alarcón' 2014, 
  <doi:10.2478/bile-2014-0006>).

Classes and methods for handling genetic data. Includes
        classes to represent genotypes and haplotypes at single markers
        up to multiple markers on multiple chromosomes. Function
        include allele frequencies, flagging homo/heterozygotes,
        flagging carriers of certain alleles, estimating and testing
        for Hardy-Weinberg disequilibrium, estimating and testing for
        linkage disequilibrium, ...

Finds subsets of sets of genotypes with a high Heterozygosity, and Mean of Transformed Kinships (MTK), measures that can indicate a subset would be beneficial for rare-trait discovery and genome-wide association scanning, respectively.

Implementation of spatial graph-theoretic genetic gravity models.
    The model framework is applicable for other types of spatial flow questions.
    Includes functions for constructing spatial graphs, sampling and summarizing
    associated raster variables and building unconstrained and singly constrained
    gravity models.

Provides tools for plotting gene clusters and transcripts by 
  importing data from GenBank, FASTA, and GFF files. It performs BLASTP and 
  MUMmer alignments [Altschul et al. (1990) <doi:10.1016/S0022-2836(05)80360-2>;
  Delcher et al. (1999) <doi:10.1093/nar/27.11.2369>] and displays results on 
  gene arrow maps. Extensive customization options are available, including 
  legends, labels, annotations, scales, colors, tooltips, and more.