Mt Fairweather NANUQ
Elizabeth S. Allman
• Mathematics and Statistics
• UAF, Fairbanks, AK
• e.allman AT alaska.edu

  • MSCquartets v. 3.3
    MSCquartets: Analyzing Gene Tree Quartets under the Multi-species Coalescent.
    joint with Hector Banos-Cervantes, Jonathan Mitchell, J.A.Rhodes, K. Wicke (R package).   CRAN download.  

          Please cite:  
    J.A. Rhodes, H.D. Banos-Cervantes, J.D. Mitchell and E.S. Allman, " MSCquartets 1.0: Quartet methods for species trees and networks under the multispecies coalescent model in R. " Bioinformatics, 37 no. 12 (1766–1768), 2021.   online

          Other relevant and helpful citations include:
    "Gene tree discord, simplex plots, and statistical tests under the coalescent." E.S. Allman, J.D. Mitchell and J. Rhodes, Syst. Biol., 71 no. 4 (2022) 929-942. https://doi.org/10.1093/sysbio/syab008">doi.

    "NANUQ: A method for inferring species networks from gene trees under the coalescent model," E.S. Allman, H. Banos-Cervantes and J.Rhodes, Algorithms for Molecular Biology, 14 no. 24 (2019).   online

    "Hypothesis testing near singularities and boundaries," E.S. Allman, J. Mitchell and J.Rhodes, Electronic Journal of Statistics, 13 no. 1 (2019) 1250-1293.

  • SymbolicQuartetCF v. 0.1.7
    S. Kong, with A. Englander, J. Garbett, and I. Nometa. (Julia package) available at GitHub.
    Computes symbolic quartet concordance factors under the Network Multispecies Coalescent Model.

  • PhyloCoalSimulations
    C. Ane and J. Fogg. (Julia package) available at JuliaPhylo.
          Please cite:  
    "PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow." with J. Fogg and C. Ane, Syst. Biol., 72 (5) 1171-1179. (2023). doi

  • MSCsimtester v. 1.0.
    Joint with Hector Banos-Cervantes and J.A. Rhodes. (R package) available on CRAN.
          Please cite:   Allman, Elizabeth S., Banos, Hector D., and Rhodes, John A.. Testing Multispecies Coalescent Simulators using Summary Statistics. IEEE/ACM Transactions on Computational Biology and Bioinformatics. doi:10.1109/TCBB.2022.3177956

  • SplitSup v. 1.02.
    Download from GitHub or in zip format.
          Please cite the following paper if you use SplitSup in your research:
    Split scores: a tool to quantify phylogenetic signal in genome-scale data with L. Kubatko and J. Rhodes. with L.S. Kubatko and J.A.Rhodes, Systematic Biology, 66 no.4 (2017) 620-636.