In this work, the clustering presented above was based on matrices S computed from whole 250 ns MD trajectories.
IFC clustering algorithm will compute the fuzzy membership degree matrix based on the optimal cluster centers and, meanwhile, clusters are divided according to the membership degree matrix to obtain the clustering results in the end.
Based on this matrix, successive clustering of lineages was done to construct the unrooted phylogenetic tree of all potential AMPs gene using the maximum-likelihood algorithm with 1000 bootstrap replicates.
Based on the presence/absence matrix, clustering of strains from different pathovars could be linked in some cases to the host plant.
Based on this matrix, a hierarchical clustering was conducted by the program AGNES (agglomerative hierarchical clustering algorithms) where proteins are clustered closer if their protein sequences have higher similarity (Materials and Methods) [ 27].
In the first step, we estimate the mixing matrix based on hierarchical clustering, assuming that the source signals are sufficiently sparse.
In specially, the research of clustering nonlinear correlation data object is rare, so we propose Matrix Similarity Clustering Algorithm (MSCA) based on random matrix theory and combined with sliding window technology to cluster the similarity of multidimensional time sequences.
Although our clustering was based on the matrix of regulatory influence, the clusters also provided a strong basis for interpreting gene expression.
A group-average cluster analysis was conducted with the Bray-Curtis similarity matrix and, based on the generated cluster dendrogram, a 25% similarity threshold was superimposed on the nMDS ordinations for the rehabilitated and reference sites.
Then, we converted the Tanimoto similarity matrix into distance matrix by subtracting each of the similarity values from 1. Based on distance matrix, we performed heatmap clustering and the result is shown in Figure 9. White and red colours indicate the extreme distance values of 0 and 1, respectively, and the intermediate distance values are indicated by the intensity of the red colour.
