Summarising information content

[ms609]

https://academic.oup.com/bioinformatics/article/37/16/2325/6131675

• Long branch score
  • For each taxon, it's patristic distance from taxon i to all other taxa, over mean patristic distance across all taxa, times 100. Ref: Struck, 2014; Weigert et al., 2014.
• Saturation

  Saturation is estimated from the slope of the regression line between patristic distances and pairwise identities.Saturated MSAs have reduced phylogenetic information and can result in issues of long branch attraction (Lake, 1991; Philippe et al., 2011).

• Treeness (aka Stemminess)

  a measure of the inferred relative amount or rate of evolutionary change that has taken place on internal branches of a phylogenetic tree (Lanyon, 1988; Phillips and Penny, 2003)

  • = proportion of tree length that occurs on internal branches