98%
921
2 minutes
20
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11057537 | PMC |
http://dx.doi.org/10.1089/cmb.2023.0312 | DOI Listing |
Causal relationships between different entities are often modeled as labeled acyclic digraphs (DAGs) in biology and healthcare, in particular for depicting the progression of malignant tumor cells. Comparison of labeled DAGs is essential for developing methods for inference and evaluation of DAG models. Therefore, a robust dissimilarity metric is critical for such comparison tasks.
View Article and Find Full Text PDFAlgorithms Mol Biol
August 2025
Department of Computer Science, University of Sherbrooke, 2500 Bd de l'Université, J1K2R1, Sherbrooke, QC, Canada.
Background: In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies differences in the topology of reconciled gene trees, but also considers discrepancies in predicted ancestral gene-species maps and speciation/duplication events, offering a refinement of existing metrics such as Robinson-Foulds (RF) and their labeled extensions LRF and ELRF. A tunable parameter also allows users to adjust the balance between its species map and event labeling components.
View Article and Find Full Text PDFSemidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define here a general class of semidirected phylogenetic networks, with a stable set of leaves, tree nodes and hybrid nodes.
View Article and Find Full Text PDFJ Comput Biol
July 2025
Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
Motivated by applications in medical bioinformatics, Khayatian et al. (2024) introduced a family of metrics on Cayley trees [the -Robinson-Foulds (RF) distance, for . .
View Article and Find Full Text PDFPhylogenetic trees represent the evolutionary relationships and ancestry of various species or groups of organisms. Comparing these trees by measuring the distance between them is essential for applications such as tree clustering and the Tree of Life project. Many distance metrics for phylogenetic trees focus on trees defined on the same set of taxa.
View Article and Find Full Text PDF