title: AlphaMPSim: flexible simulation of multi-parent crosses.
abstract: Multi-parent crosses of recombinant inbred lines exist in many species for fine-scale analysis of genome structure and marker-trait association. These populations encompass a wide range of crossing designs with varying potential. AlphaMPSim is a flexible simulation program that is efficiently designed for comparison of alternative designs for traits with varying genetic architectures and biallelic markers with densities up to full sequence. A large pool of founder haplotypes can be supplied by the user, or generated via integration with external coalescent simulation programs such as MaCS. From these, diverse founders for multi-parent designs can be generated automatically, and users can compare designs generated from diverse pedigrees. Full tracking of identity by descent status of alleles within the pedigree is undertaken, and output files are compatible with commonly available analysis packages in R.
  
  
  METHODS
  Executable versions of AlphaMPSim for Mac and Linux and a user manual are available at http://www.roslin.ed.ac.uk/john-hickey/software-packages/.
authors.affiliation: The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 México D.F. and CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia.
authors.forename: John M
authors.initials: JM
authors.lastname: Hickey
authors.affiliation: The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 México D.F. and CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia.
authors.forename: Gregor
authors.initials: G
authors.lastname: Gorjanc
authors.affiliation: The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 México D.F. and CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia.
authors.forename: Sarah
authors.initials: S
authors.lastname: Hearne
authors.affiliation: The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 México D.F. and CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia.
authors.forename: Bevan E
authors.initials: BE
authors.lastname: Huang
mesh_terms: D023281:Genomics / Q000379:methods*; D006239:Haplotypes; D006824:Hybridization, Genetic; D007178:Inbreeding; D008957:Models, Genetic; D010641:Phenotype; D012984:Software