MSCsimtester: An R package for testing simulators of the multispecies coalescent process.
For examples and citation, see "Testing Multispecies Coalescent Simulators using Summary Statistics", E.S. Allman, H. Banos, J.A. Rhodes, 2019
R package: MSCsimtester_1.0.0.tar.gz
Manual: MSCsimtester_1.0.0.pdf
MSCquartets: An R package for analyzing a collection of gene trees under the tree/network multispecies coalescent model through displayed quartets. Version 1.0.5 is now available on CRAN, at https://cran.r-project.org/web/packages/MSCquartets/
The package includes methods developed in the papers:
[R19] Toplogical metrizations of trees and new quartet methods of tree inference, J.A. Rhodes, IEEE/ACM Trans. Comput. Biol. Bioinf., early access, 2019 https://doi.org/10.1109/TCBB.2019.2917204
[MAR19] Hypothesis testing near singularities and bondaries, J.D. Mitchell, E.S. Allman, J.A. Rhodes, Electron. J. Statist., 13 (1) 2019 https://projecteuclid.org/euclid.ejs/1561687407
[YR19] Inferring metric trees from weighted quartets via an intertaxon distance, S. Yourdkhani, J.A. Rhodes, 2020
[ABR19] NANUQ: A method for inferring species networks from gene trees under the coalescent model, E.S. Allman, H. Banos, J.A. Rhodes, Algorithms Mol. Biol., 14 (24) 2019 https://doi.org/10.1186/s13015-019-0159-2
Scripts for Yourdkhani & Rhodes (2020): R scripts and related files for the simulation analysis of Inferring metric trees from weighted quartets via an intertaxon distance are available here. See comments at beginnings of script files for instructions before running them.