Functions to infer co-mapping trait hotspots and causal models.
  Chaibub Neto E, Keller MP, Broman AF, Attie AD, Jansen RC, Broman KW, Yandell BS (2012) 
  Quantile-based permutation thresholds for QTL hotspots. Genetics 191 : 1355-1365. 
  <doi:10.1534/genetics.112.139451>.
  Chaibub Neto E, Broman AT, Keller MP, Attie AD, Zhang B, Zhu J, Yandell BS (2013)
  Modeling causality for pairs of phenotypes in system genetics. Genetics 193 : 1003-1013.
  <doi:10.1534/genetics.112.147124>.

Provides tools for joint analysis of multiple traits in a backcross (BC) or recombinant inbred lines (RIL) population. It can be used to select an optimal subset of traits for multiple-trait mapping, analyze multiple traits via the SURE model, which can associate different QTL with different traits, and perform multiple-trait composite multiple-interval mapping.

Functions to Simultaneously Infer Causal Graphs and Genetic Architecture.
  Includes acyclic and cyclic graphs for data from an experimental cross with a modest number (<10) of phenotypes driven by
  a few genetic loci (QTL).
  Chaibub Neto E, Keller MP, Attie AD, Yandell BS (2010)
  Causal Graphical Models in Systems Genetics: a unified framework for joint inference of causal network and genetic architecture for correlated phenotypes.
  Annals of Applied Statistics 4: 320-339.
  <doi:10.1214/09-AOAS288>.

Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.

This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances.