Datasets for testing accuracy of microbial gene tree rooting methods
The following simulated and biological datasets were used in the paper cited below to test the accuracy of various gene tree rooting methods on microbial gene families. The paper contains a detailed description of these datasets.
Assessing the Accuracy of Phylogenetic Rooting Methods on Prokaryotic Gene Families
Taylor Wade, L. Thiberio Rangel, Soumya Kundu, Gregory P. Fournier, Mukul S. Bansal.
PLOS One, 15(5): e0232950, 2020.
Simulated datasets for testing DTRL reconciliation algorithms and classification of additive and replacing transfers
The following simulated datasets contain gene trees and species trees where the gene trees were evolved inside the species tree with gene duplications, additive transfers, replacing transfers, and gene losses, using the SaGePhy simulation framework. These datasets were used in the paper cited below to test the accuracy of a heuristic for classifying transfer events inferred through DTL reconciliation as being additive or replacing. The paper contains a detailed description of these datasets.
Simulated datasets: DTRL_simulatedData.zip
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation
Misagh Kordi, Soumya Kundu, Mukul S. Bansal.
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) 2019; Proceedings, pages 514-523..