Using the gamma correction with phylogenetic analysis
What is gamma correction and how should it be used in generating phylogenetic trees?
Upon selecting the Distance Options button for Phylogenetic Reconstruction, it is apparent that the gamma correction can be either on or off and the value of the Gamma shape parameter can be specified.
Gamma correction should be used when the substitution rate varies extensively from site to site.
Gamma correction is useful with alignments in which substitutions occur at only a few sites. In this case, the true amount of change may be underestimated.
If the proportion of substituted sites is very low, use a gamma shape parameter that is closer to 1. If the distribution of variation along an alignment looks less skewed, use a value closer to 0. Don't use the correction if substitutions appear to be evenly distributed across all sites.
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