mmollina/Autopolyploid_Linkage

This repository hosts codes and analytic procedures for the article "Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models" by Mollinari and Garcia

Supplementary scripts for the paper "Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models"

by Mollinari and Garcia (2019) - DOI: 10.1534/g3.119.400378 - available here

Before performing analysis and simulations, please install:

• MAPpoly, available here
• PedigreeSim, available here
• polymapR, available here

R scripts:

• Auxiliary functions for Supporting Information 3
• Example in Supporting Information 3
• R script for Simulation 1
• R script for Simulation 2
• R script for Building SolCAP map
• Phased SolCAP denovo map
• R script for comparison study