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    • phyletica.github.io
      HTML
      2000Updated Jan 5, 2026Jan 5, 2026
    • A repo for building a Docker image running ecoevolity
      Dockerfile
      0000Updated Jan 4, 2026Jan 4, 2026
    • Estimating evolutionary coevality
      C++
      3800Updated Jan 2, 2026Jan 2, 2026
    • Repo for testing github actions.
      C++
      3000Updated Jan 2, 2026Jan 2, 2026
    • A python package for summarizing the output of Ecoevolity
      Python
      0100Updated Jan 2, 2026Jan 2, 2026
    • TeX files for the Phyletica Lab project at http://phyletica.org/codiv-sanger-bake-off
      TeX
      0000Updated Nov 26, 2025Nov 26, 2025
    • Comparing approximate and full-likelihood approaches to estimating temporal clustering of divergence times among taxa.
      Shell
      0000Updated Aug 19, 2025Aug 19, 2025
    • Machine learning experiments with state-dependent birth-death models with shared and multifurcating divergences
      Python
      0000Updated Jun 22, 2025Jun 22, 2025
    • namu

      Public
      Phylo experiment
      C++
      0000Updated Jun 11, 2025Jun 11, 2025
    • SDSDsim

      Public
      Simulating trees under a state-dependent birth-death process with shared and divergences
      Python
      0000Updated Mar 5, 2025Mar 5, 2025
    • TeX files for the Phyletica Lab project at http://phyletica.org/ecoevolity-model-prior
      TeX
      0000Updated Jan 17, 2025Jan 17, 2025
    • Analyses exploring the behavior of new comparative biogeographical model priors.
      Shell
      0100Updated Dec 20, 2024Dec 20, 2024
    • hmmer

      Public
      HMMER: biological sequence analysis using profile HMMs (fork to report forward and Viterbi scores)
      C
      86000Updated Jul 12, 2023Jul 12, 2023
    • Laboratory protocols used in the Phyletica Lab at Auburn University
      2600Updated Nov 8, 2022Nov 8, 2022
    • Analyses exploring the behavior of generalized Bayesian phylogenetics
      R
      0000Updated Jun 7, 2022Jun 7, 2022
    • gekgo

      Public
      Comparative phylogenetics of Philippine gekkonids
      HTML
      0100Updated Aug 19, 2021Aug 19, 2021
    • LaTeX (tikz) and Bash code for creating animated examples of shared divergences.
      TeX
      0000Updated Jul 29, 2021Jul 29, 2021
    • Bayesian probability of flipping lizrds.
      Jupyter Notebook
      0000Updated Jun 17, 2021Jun 17, 2021
    • Simulation experiments to explore statistical behavior of estimating shared demographic changes.
      TeX
      0000Updated Jun 30, 2020Jun 30, 2020
    • Simulations to assess performance of ecoevolity conditional on Sumatran frog genomic data.
      Python
      0000Updated May 12, 2020May 12, 2020
    • A repo for testing the efficiency of MCMC operators implemented in ecoevolity.
      Shell
      0000Updated Feb 17, 2020Feb 17, 2020
    • Analyses exploring the behavior of Ecoevolity, a method for estimating shared evolutionary events.
      TeX
      0000Updated Jan 29, 2020Jan 29, 2020
    • Simulation-based experiments to assess how ecoevolity handles single-locus datasets.
      TeX
      0000Updated Dec 16, 2019Dec 16, 2019
    • Materials for teaching evolution for the Alabama Prison Arts + Education Project (APAEP)
      TeX
      0000Updated Nov 7, 2019Nov 7, 2019
    • Shell and R code to create animated gif of sea level change.
      R
      0100Updated Apr 11, 2019Apr 11, 2019
    • Some thoughts on Dirichlet and Pitman-Yor processes and possible extensions of them.
      TeX
      0000Updated Mar 8, 2019Mar 8, 2019
    • Simulation-based test of general linear model marginal likelihood method
      Shell
      0100Updated Jan 15, 2019Jan 15, 2019
    • A web implementation of fragcoalsim
      HTML
      0000Updated Sep 19, 2018Sep 19, 2018
    • A demonstration of Bayesian statistics
      Python
      1100Updated Aug 14, 2018Aug 14, 2018
    • Example data for running ecoevolity
      0000Updated May 24, 2018May 24, 2018