Phylogenetics and Sequence Analysis

Four traps that produce a confidently wrong number

Each of these was observed producing a wrong answer while the correct guidance was already present further down this file. Check them before you answer.

1. PhyKIT prints more than one column, and for saturation the two conventions disagree — state which you used. phykit saturation prints saturation <TAB> |saturation-1|. Its own --help is explicit: "The first value is the saturation value and the second column is the absolute value of saturation minus 1." But several published analyses (and some reference answers derived from them) report the second column as "the saturation value". The two always sum to 1.0000, which is the tell that you may be looking at the wrong one — on the fungal scogs set the medians are 0.39 (col 1) and 0.61 (col 2).