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The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.
We may thus expect estimates of selective constraint to be lower for more distant comparisons.
Estimates of selective pressure suggest unspecific recognition of the proline-rich domain by cytoskeletal proteins.
Alternatively, estimates of selective pressures acting on such genes might indicate whether functionality is preserved [ 22- 26].
Estimates of selective constraints obtained with muscle and cmalign are shown in supplementary tables S2 and S3 (Supplementary Material online), respectively.
Thus, it remains a great challenge in current research to provide analytical, experimental, or computational estimates of selective pressures acting on individual proteins.
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Note that if selection pressures alternative to translational selection affect synonymous (and optimal) codon use, this may lead to under- or over-estimates of selective strength on optimal codon use depending on strength and direction of translational selection.
However, only one estimate of selective logging was available with statewide coverage over multiple years [4].
Depending on strength and direction of translational selection in an organism, such alternative selective forces may lead to under- or over-estimates of selective strength on optimal codon use.
However, only one estimate of selective logging was available with statewide coverage over multiple years [ 4]. [ 4] estimated that selective logging in Mato Grosso averaged 9,367 km2 yr-1 during 1999-2002.
The first is motivated by weakly deleterious mutations that segregate transiently in the population, which are known to inflate the estimate of selective constraint and cause underestimation of the number of adaptive substitutions [ 34].
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