2024
DOI: 10.7717/peerj.18504
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PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

Wayne P. Maddison

Abstract: In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming tool, PhyIN, which deletes regions in which a large proportion of sites (characters) have conflicting phylogenetic signal. It does not require inference of a phylogenetic tree, as it finds neighbouring characters that cannot agree on any possible tree. In phylogenomic data of ultraconserved elements (UCE), PhyIN … Show more

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