Six-state amino acid recoding is not an effective strategy to offset compositional heterogeneity and saturation in phylogenetic analyses

Alexandra Hernandez & Joseph Ryan
Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In our simulation analyses, non-recoding approaches...
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3 downloads reported since publication in 2021.

These counts follow the COUNTER Code of Practice, meaning that Internet robots and repeats within a certain time frame are excluded.
What does this mean?