Numerical stiffnesses are presented for three problems which adequately cover the alternative (parameter-dependent) forms which the explicit expressions can take.
The optimization of the likelihood surface for phylogenetics problems is complex and we have started experimenting with the alternative parameter optimizers available in NLopt (http://ab-initio.mit.edu/wiki/index.php/NLopt).edu/wiki/index.php/NLopt
However, to justify the usage of any of these alternative parameters is difficult.
One of these alternative parameters focuses on the overall number of lymph nodes retrieved.
This study compared these alternative parameters with conventional TNM staging in predicting long-term survival in patients undergoing curative resection.
We provide the corresponding R code in Additional file 7. Bins containing a read count of 0 in both samples of a pair contain no information and were therefore excluded from the comparative analyses of SERE and the two alternative parameters described below.
It would seem more realistic to use the mass loss of the single step (B) instead (A + B), and of course the step C, that is (see Table 2) to use the simplified alternative parameters (B) and (B/C).
The results on alternative parameters reviewed in the literature usually address less complex and sub lethal reactions (e.g. determination of specific enzymes or gene activities) at a level of a single or some individuals, often resulting in an increased sensitivity.
