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Since the CCC is often used on data sets where no meaningful pairwise distance function can be given, the question remains of cohesion within a cluster can be meaningfully defined.
In an analysis of 16 complete γ-proteobacteria genomes, we also illustrate how the signature method can also be used on data sets in which some of gene sequences are missing.
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These approaches are sensitive to saturation of synonymous sites (Smith JM and Smith NH 1996), and therefore most suitable for use on data sets containing closely related sequences (Anisimova and Liberles 2007).
All three methods are shown to be successful to an extent, although a critical comparison indicates reservations about the density estimation approach when used on sparse data sets.
Refined IBD is computationally efficient and can be used on large data sets.
Reference-free 2D classification in IMAGIC was subsequently used on the data sets to remove averages with blurred appearance or incorrect size.
This study suggests that there is a need for well-conducted validation studies to establish optimal statistical techniques to be used on such data sets.
This approach is used on small data sets as the traditional "statistical significance" methods may result in p values > 0.05 to 0.1.
Though the models can get a good performance during cross-validation, they may have problems when used on new data sets or applications.
Non ML methods were also used on these data sets using MEGA version 3.1 [ 79], parsimony, and Neighbour Joining with the LogDet distance, in an attempt to overcome the problem of mutual attraction of the branches which have the same compositional bias.
Furthermore, the methodology of transductive SVMs [41] could be used to enable training on data sets with missing labels.
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