In summary, in spite of tremendous methodological and algorithmic advances, even the fastest existing algorithms for DTL reconciliation (David and Alm, 2011; Merkle et al., 2010) as well as for tcDTL reconciliation on fully dated trees (Doyon et al., 2010) still have a time complexity of Θ(mn).
The paper outlines both the methodological and algorithmic aspects of the modelling, forecasting and signal extraction procedures, including the design and implementation of forecasting support software with a specially designed Graphical User Interface within the Matlab® computing environment.
This should motivate further investigations on related methodological and algorithmic problems.
Although methodological and algorithmic limitations may have precluded the use of phylogenetic networks in the past, a few steps have been taken in this direction [ 123].
Our main objective is therefore to propose methodological and algorithmic improvements and parallelization strategies to compute the PLF without modifying the underlying evolutionary model.
