diff --git a/docs/usage/index.rst b/docs/usage/index.rst index 51b24d8..0b31de8 100644 --- a/docs/usage/index.rst +++ b/docs/usage/index.rst @@ -290,7 +290,7 @@ Compositional bias per site ########################### Function names: compositional_bias_per_site; comp_bias_per_site; cbps |br| -Command line interface: pk_compositional_bias_per_site; pk_compositional_bias_per_site; pk_cbps +Command line interface: pk_compositional_bias_per_site; pk_comp_bias_per_site; pk_cbps Calculates compositional bias per site in an alignment. @@ -1337,9 +1337,9 @@ Calculate treeness statistic for a phylogeny. Higher treeness values are thought to be desirable because they represent a higher signal-to-noise ratio. -Treeness describes the proportion of the tree distance found on -internal branches. Treeness can be used as a measure of the -signal-to-noise ratio in a phylogeny. +Treeness is the sum of internal branch lengths divided by the total +tree length. Therefore, values range from 0 to 1. Treeness can be +used as a measure of the signal-to-noise ratio in a phylogeny. Calculate treeness (also referred to as stemminess) following Lanyon, The Auk (1988), doi: 10.1093/auk/105.3.565 and