2022
DOI: 10.1101/2022.07.21.501007
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AutoPhy: Automated phylogenetic identification of novel protein subfamilies

Abstract: Phylogenetic analysis of protein sequences provides a powerful means of identifying novel protein functions and subfamilies and for identifying and resolving annotation errors. However, automation of functional clustering based on phylogenetic trees has been challenging, and most of it is done manually. Clustering phylogenetic trees usually requires the delineation of tree-based thresholds (e.g., distances), leading to an ad hoc problem. We propose a new phylogenetic clustering approach that identifies cluster… Show more

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“…To address this issue, Ortiz-Velez et al developed AutoPhy [6], an automated approach that combines phylogenetic analysis, dimensionality reduction, and clustering techniques to identify protein subfamilies with distinct functional roles. AutoPhy enables the detection of functionally diverse subfamilies within larger protein families, facilitating the discovery of novel protein functions.…”
Section: Introductionmentioning
confidence: 99%
“…To address this issue, Ortiz-Velez et al developed AutoPhy [6], an automated approach that combines phylogenetic analysis, dimensionality reduction, and clustering techniques to identify protein subfamilies with distinct functional roles. AutoPhy enables the detection of functionally diverse subfamilies within larger protein families, facilitating the discovery of novel protein functions.…”
Section: Introductionmentioning
confidence: 99%