In this paper, we employ multi-parametric (mp) programming to move most of the computation offline, thus allowing the application of the closed-loop approach to fast processes.
Using the Open MP programming paradigm, several loops charge calculation for multiple molecules, evaluation over different (kappa) values in the LR method, and minimization of multiple parameter sets in DE-MIN run in parallel on available CPU cores.
MP designed, programmed and implemented the application and drafted the manuscript.
Finally, to account for potential discordances between gene trees and the species tree, we used the pseudo-ML approach implemented in the MP-EST program [ 83].
The STAR and MP-EST programs were run using several different subsets of loci.
Phylogenetic analyses were performed using neighbor joining (NJ), maximum parsimony (MP) in the program MEGA version 5.1 [ 38] and using maximum likelihood (ML) in the program PhyML version 3.0 [ 39].
In the operation of the minimalist program (MP), agreement is considered a by-product of case assignment.
By formulating the worst-case WSR maximization problem into a monotonic program (MP), we develop a polyblock outer approximation algorithm to obtain the globally optimal solution.
Furthermore, the chapter illustrates the creation of an application-level multicast ping program (mping).
