our inability to reliably infer branch lengths and substitution parameters.
However, sequences that are too divergent could lead to saturation, i.e. Phylogenetic tree should be at least one expected substitution per codon site, but it is impossible to give a generally valid range for desirable sequence divergence. Yang and colleagues have suggested that the total length of the Sequence along a star phylogeny) sample of the Human T-lymphotropic virus (HTLV), they found that the method performed poorly. For example when, Suzuki and Nei applied a REL-type method to a very low divergence (1 or 2 substitutions per Sequence diversity is needed for reliable inference. Because comparative methods estimate relative rates of synonymous and non-synonymous substitution, substantial Influenza A viruses infecting different individuals). mammalian interferon genes), or a diverse population sample
Ideally, the alignment should represent a single gene, or protein product, sampled over multiple taxa (e.g. To perform a selection analysis, needs a multiple alignment of at least three homologous coding nucleotide sequences.Ĭodon based methods for estimating dN and dS can be applied to any sequence alignment, but there are several considerations to keep in mind:
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