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The traditional HMMs with K = 10, 13, 16 states are also compared for which a Matlab toolbox for HMM written by K. Murphy was used in its default setting (http://www.cs.ubc.ca/murphyk/Software/HMM/hmm.html ) except that the full covariance matrix is assumed.
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Often, multiple groups each containing several individuals are compared for traits which may differ only quantitatively but not qualitatively.
Retained alignments were compared for SNPs, which were tentatively separated into two alleles at the same locus.
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This assured that we only compared codons for which there is strong evidence of homology across all 12 species.
The ANN and RSM model were compared for DoE, using which the both models were prepared.
The results are compared for cases in which both methods may be used.
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