Jacob L. Steenwyk, Thomas J. Buida, Yuanning Li, Xing-Xing Shen, Antonis Rokas

Highly divergent sites in multiple sequence alignments, which stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Trimming methods aim to remove these sites before phylogenetic inference, but recent analysis suggests that doing so can worsen inference. We introduce ClipKIT, a trimming method that instead aims to retain phylogenetically-informative sites; phylogenetic inference using ClipKIT-trimmed alignments is accurate, robust, and time-saving.