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Using the data obtained by GeneChip 430 2.0 microarray analysis, we performed hierarchical clustering using the GeneSpring GX7.3 software and constructed a dendrogram for the 87 samples (Figure 1A).
We then made profiles for individual subtypes and features, calculated the distance matrices, and constructed a dendrogram for each feature.
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To test the hypothesis of a correspondence between repertoires of T3Es and pathovars, we constructed a dendrogram from a matrice summarizing presence/absence of the T3Es for each of the 132 selected strains.
Correlation coefficients were used to construct a dendrogram of similarities between the different indices.
Based on the presence/absence matrix of T3E genes for each of the 132 strains of X. axonopodis, we constructed a dendrogram using Jaccard distances and Neighbor-Joining method.
To search for homologous sequences in the GenBank database, we performed a BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) analysis and constructed a dendrogram based on 16S rDNA sequences of A. bovis (10 ).
The position tolerance for selection of bands in constructing a dendrogram was kept constant at 1% through out the interpretations.
These coefficients were utilized to construct a dendrogram using the UPGMA.
The levels of similarity at which observations are merged are used to construct a dendrogram.
The pair-wise distances between points, indicating similarity between images, were used to construct a dendrogram (Fig. 2B).
Euclidean distance matrix was computed for evaluation of genetic distances between genotypes and further utilized to construct a dendrogram using the neighbour joining method [ 34].
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