If the number of classes C is too small, the method does not resolve the clusters at fine grain.
Thus congruency in the phylogenies of human HOX clusters and SP genes not only resolved the cluster duplication events but also decisively rejected the assumption that four HOX clusters in tetrapods are the result of two rounds of whole genome duplication early in vertebrate history.
The importance of resolving the clusters based on all 5 components simultaneously can be appreciated by examining all possible two-component projections of the clusters composition (Fig. 3, left).
Starting with the clusters as crude groupings of associated genes, we used PCA to segregate each of these into several principal components (PCs), thus resolving the clusters into subclusters.
Although there is one gymnosperm genome P. abies available, Figure 1 suggests that more gymnosperm sequences are needed to resolve the uncertain clustering of P. abies homologs in CslB/H/E/J/G clusters.
These gene trees failed to resolve the species clusters obtained using the concatenated sequences and all individual trees showed anomalous clustering of some strains.
The amino acid variation does not correlate with cluster allegiance, so that amino acid based phylogenies of the different actin gene copies do not resolve the two clusters (data not shown).
Results from a case study in Anshun, China reveal that the proposed approach outperforms the other three prevailing algorithms to resolve the customer clustering problem.
