Similarities were converted into distances by applying the formula 1 – (pairwise avg. ANIb/100).
Sequence divergence for each gene was calculated by applying the Jukes Cantor correction for the pairwise nucleotide differences.
The core of MMDA is to maximize the between-class margin on the decision boundary by applying the normals of a set of pairwise orthogonal margin maximizing hyperplanes to construct a projection subspace.
Initial tree(s) for the heuristic search were obtained by applying the BioNJ method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach.
Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach.
Initial tree(s) for the heuristic search were obtained by applying the neighbor-joining method to a matrix of pairwise distances estimated using the maximum composite likelihood approach.
Initial trees for the heuristic search were obtained by applying the Neighbour-Joining method to the matrix of pairwise distances estimated using a JTT model [ 49].
Initial tree(s) for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using a JTT model.
Such a model is obtained from information theoretic considerations by applying the principle of maximum entropy methods)[15]. Models of pairwise network connectivity obtained from entropy maximization have proven insightful in different and seemingly disparate contexts[16], [17].
Their method consists in identifying pairwise Granger causality between gene expression time series and then, by applying the method proposed by Bader and Hogue (2003), to detect dense regions in the network.
