Cliping and Keeping Information Trimmer (ClipKIT) was developed as part of Jacob L. Steenwyk’s graduate thesis work.

Since the early 1990’s, multiple sequence alignments have been filtered or “trimmed” to remove sites that may cause errors in phylogenetic inference. Errors can be caused by erroneously inferring site homology or saturation of multiple substitutions, both of which often present as highly divergent sites. However, recent analysis by Tan et al. (2015) revealed current methods of alignment trimming often resulted in worse phylogenetic inferences. These findings highlight the need for alternative MSA trimming strategies.

In light of these findings, we developed ClipKIT, which implements an innovative yet simple trimming strategy. ClipKIT achieves this by identifying and retaining phylogenetically-informative sites rather than identifying and trimming highly divergent ones. Our assessments of ClipKIT’s performance using empirical datasets of Mammalian and Yeast sequences and simulated sequences from metazoans, flowering plants, filamentous fungi, and budding yeasts (see details here) suggests ClipKIT is a top-performing software.

The Developers

ClipKIT is developed and maintained by Jacob L. Steenwyk and Thomas J. Buida III.


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Jacob L. Steenwyk is a Howard Hughes Medical Institute Gilliam fellow in the Antonis Rokas Laboratory at Vanderbilt University. His research foci include understanding the parameters that influence genome stability, the genomics of microbial domestication, and the evolution of pathogenicity. Beyond research, Steenwyk aims to make education more accessible through diverse avenues of community engagement. Find out more information at his personal website.


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Thomas J. Buida III is a senior software and data engineer at Initial State. His main interests are in the design and execution of elegant solutions to complex data problems. His expertise lies in backend software development. Flagship side projects include twitch-top-eight, a panel extension to view top viewers/streamers, and Hue Kolorize, a Hue light extension that matches the dominant color extracted from a flexible source to the Hue light color. Find out more information at his personal website.

More Team Members

ClipKIT has been made possible by other key personnel including Antonis Rokas, Yuanning Li, and Xing-Xing Shen.


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Antonis Rokas is the Cornelius Vanderbilt Chair in Biological Sciences and Director of the Evolutionary Studies Initiative at Vanderbilt University. Research in his laboratory focuses on the study of the DNA record to gain insight into the patterns and processes of evolution. Using a combination of computational and experimental approaches, his lab’s current research aims to understand the molecular foundations of the fungal lifestyle, the reconstruction of the tree of life, and the evolution of human pregnancy. Find out more information at his laboratory’s website.


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Xing-Xing Shen is an Assistant Professor of Institute of Insect Sciences at Zhejiang University. His lab is broadly interested in evolutionary biology, phylogenetics, comparative genomics, and bioinformatics. His current research mainly focus on: 1) investigating phylogenetic relationships in animals and fungi using genome-scale data; 2) identifying the factors that lead to phylogenetic incongruence; and 3) exploring insect species and ecological diversity. Find out more information at his laboratory’s website.

Information about other team members coming soon!