mappoly2 (V.2.0.0): Construction of genetic maps in interconnected full-sib autopolyploid families including mixed ploidy levels

MAPpoly2 is an R package designed to build maps in interconnected full-sib autopolyploid families. It has been enhanced for user-friendliness and accessibility. This version, developed for potential integration with R Shiny, aims to provide a user-intuitive interface for genetic mapping in polyploids. It can handle ploidy levels of 2, 4, and 6, including any combination of these.

One of the key improvements in MAPpoly2 is its enhanced performance, largely due to the implementation of computationally intensive codes primarily in C++. This enables efficient handling of large datasets. Additionally, the package facilitates the construction of individual maps for each parent using a Hidden Markov Model (HMM), significantly speeding up the map construction process. These individual maps can then be merged, and a joint map is recomputed to include any remaining markers.