ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be…

• NS
  National Science Foundation

  Awards: DEB-1442113, 1442113
• HH
  Howard Hughes Medical Institute
• BW
  Burroughs Wellcome Fund
• JS
  John Simon Guggenheim Memorial Foundation
• ZU
  Zhejiang University
• NI
  National Institutes of Health
• NS
  National Science Foundation of Sri Lanka

  Award: DEB-1442113
• FR
  Fundamental Research Funds for the Central Universities
• NI
  National Institute of Allergy and Infectious Diseases

  Awards: 1R56AI146096-01A1, R56AI146096