Steenwyk, J.; Martínez-Redondo, G.; Buida, T.; Gluck-Thaler, E.; Shen, X.; Gabaldón, T.; Rokas, A.; Fernández, R. PhyKIT: A Multitool for Phylogenomics. Preprints2024, 2024041514. https://doi.org/10.20944/preprints202404.1514.v1
APA Style
Steenwyk, J., Martínez-Redondo, G., Buida, T., Gluck-Thaler, E., Shen, X., Gabaldón, T., Rokas, A., & Fernández, R. (2024). PhyKIT: A Multitool for Phylogenomics. Preprints. https://doi.org/10.20944/preprints202404.1514.v1
Chicago/Turabian Style
Steenwyk, J., Antonis Rokas and Rosa Fernández. 2024 "PhyKIT: A Multitool for Phylogenomics" Preprints. https://doi.org/10.20944/preprints202404.1514.v1
Abstract
Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution-based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command-line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gene function prediction.
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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