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The most used initialization method is the Nearest Neighbor Method, which assigns each internal node the median solution from its three nearest leaves, using a median solver of choice.
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Although using breakpoint median solver may be faster, it can introduce gene orders with signs that is hard to deal with, due to the fact that transposition does not deal with signs at all.
We can also apply GRAPPA or MGR to obtain the phylogeny, using either breakpoint median solver or inversion median solver.
Figure 3 Simulation of the band structure using a 1D Poisson solver (Snider Poisson-Solver:http://www.nd.edu/∼gsnider/).edu/∼gsnider/
In general, an analyst is able to solve a deterministic problem using a specific solver, for instance a commercial FE-solver or an in-house solver.
All used models were input-oriented and solved using a robust solver XA from Sunset Software Technology.
Figure 8 shows the distribution of X at T = 5 calculated using a CME solver.
(d) When all gene vectors have been assigned, recalculate the profile of each cluster using a TSP solver.
The name of this file tells URDME what solver it builds; when urdme is invoked with the option to run a simulation using a specific solver, it will look for a Makefile with the correct naming pattern.
In GRAPPA-TP, we choose to use the transposition median solver in the initialization procedure as well.
We will then use our modified median solver to iteratively update the gene order of these internal nodes with those fixed adjacencies.
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