2024/12/05 by Wayne P. Maddison · 1 voice · 3 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #Artificial intelligence #Biology #Clade #Combinatorics #Computer science #Evolution and Paleontology Studies #Evolutionary biology #Gene #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Inference #Locus (genetics) #Mathematics #Phylogenetic network #Phylogenetic tree #Phylogenetics #Phylogenomics #Tree (set theory) #Trimming
paper · doi:10.7717/peerj.18504
openalex publication_date 2024/12/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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 effectively finds the boundaries between chaotic (conflicted) and orderly regions of alignments with data for only a single locus. Its ability to work on individual loci allows it to preserve discord between gene trees and species trees.