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    31 repositories

    • phyletica.github.io

      Public
      phyletica.github.io
      HTML
      •2•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • ecoevolity-docker

      Public
      A repo for building a Docker image running ecoevolity
      Dockerfile
      •0•0•0•0•Updated Jan 4, 2026Jan 4, 2026

    • ecoevolity

      Public
      Estimating evolutionary coevality
      C++
      •
      GNU General Public License v3.0
      •3•8•0•0•Updated Jan 2, 2026Jan 2, 2026

    • ecoevolity-gh-actions-testing

      Public
      Repo for testing github actions.
      C++
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Jan 2, 2026Jan 2, 2026

    • pycoevolity

      Public
      A python package for summarizing the output of Ecoevolity
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 2, 2026Jan 2, 2026

    • codiv-sanger-bake-off-tex

      Public
      TeX files for the Phyletica Lab project at http://phyletica.org/codiv-sanger-bake-off
      TeX
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • codiv-sanger-bake-off

      Public
      Comparing approximate and full-likelihood approaches to estimating temporal clustering of divergence times among taxa.
      Shell
      •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • SDSDsim-phyddle-experiments

      Public
      Machine learning experiments with state-dependent birth-death models with shared and multifurcating divergences
      Python
      •0•0•0•0•Updated Jun 22, 2025Jun 22, 2025

    • namu

      Public
      Phylo experiment
      C++
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • SDSDsim

      Public
      Simulating trees under a state-dependent birth-death process with shared and divergences
      Python
      •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • ecoevolity-model-prior-tex

      Public
      TeX files for the Phyletica Lab project at http://phyletica.org/ecoevolity-model-prior
      TeX
      •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

    • ecoevolity-model-prior

      Public
      Analyses exploring the behavior of new comparative biogeographical model priors.
      Shell
      •0•1•0•0•Updated Dec 20, 2024Dec 20, 2024

    • hmmer

      Public
      HMMER: biological sequence analysis using profile HMMs (fork to report forward and Viterbi scores)
      C
      •
      Other
      •86•0•0•0•Updated Jul 12, 2023Jul 12, 2023

    • lab-protocols

      Public
      Laboratory protocols used in the Phyletica Lab at Auburn University
      2•6•0•0•Updated Nov 8, 2022Nov 8, 2022

    • phycoeval-experiments

      Public
      Analyses exploring the behavior of generalized Bayesian phylogenetics
      R
      •
      Other
      •0•0•0•0•Updated Jun 7, 2022Jun 7, 2022

    • gekgo

      Public
      Comparative phylogenetics of Philippine gekkonids
      HTML
      •
      Other
      •0•1•0•0•Updated Aug 19, 2021Aug 19, 2021

    • tikz-codivergence-cartoons

      Public
      LaTeX (tikz) and Bash code for creating animated examples of shared divergences.
      TeX
      •
      Other
      •0•0•0•0•Updated Jul 29, 2021Jul 29, 2021

    • bayesian-lizard-flipping

      Public
      Bayesian probability of flipping lizrds.
      Jupyter Notebook
      •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

    • ecoevolity-demog-experiments

      Public
      Simulation experiments to explore statistical behavior of estimating shared demographic changes.
      TeX
      •0•0•0•0•Updated Jun 30, 2020Jun 30, 2020

    • ecoevolity-sumatran-frogs

      Public
      Simulations to assess performance of ecoevolity conditional on Sumatran frog genomic data.
      Python
      •0•0•0•0•Updated May 12, 2020May 12, 2020

    • ecoevolity-operator-tests

      Public
      A repo for testing the efficiency of MCMC operators implemented in ecoevolity.
      Shell
      •0•0•0•0•Updated Feb 17, 2020Feb 17, 2020

    • ecoevolity-experiments

      Public
      Analyses exploring the behavior of Ecoevolity, a method for estimating shared evolutionary events.
      TeX
      •0•0•0•0•Updated Jan 29, 2020Jan 29, 2020

    • ecoevolity-one-locus-experiments

      Public
      Simulation-based experiments to assess how ecoevolity handles single-locus datasets.
      TeX
      •0•0•0•0•Updated Dec 16, 2019Dec 16, 2019

    • apaep-evolution

      Public
      Materials for teaching evolution for the Alabama Prison Arts + Education Project (APAEP)
      TeX
      •
      Other
      •0•0•0•0•Updated Nov 7, 2019Nov 7, 2019

    • animating-sea-level-change

      Public
      Shell and R code to create animated gif of sea level change.
      R
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Apr 11, 2019Apr 11, 2019

    • weighted-discount-process-notes

      Public
      Some thoughts on Dirichlet and Pitman-Yor processes and possible extensions of them.
      TeX
      •0•0•0•0•Updated Mar 8, 2019Mar 8, 2019

    • abc-glm-marginal-test

      Public
      Simulation-based test of general linear model marginal likelihood method
      Shell
      •
      Creative Commons Attribution 4.0 International
      •0•1•0•0•Updated Jan 15, 2019Jan 15, 2019

    • fragcoalsim-web

      Public
      A web implementation of fragcoalsim
      HTML
      •
      GNU Lesser General Public License v3.0
      •0•0•0•0•Updated Sep 19, 2018Sep 19, 2018

    • bayes-demo

      Public
      A demonstration of Bayesian statistics
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Aug 14, 2018Aug 14, 2018

    • ecoevolity-example-data

      Public
      Example data for running ecoevolity
      0•0•0•0•Updated May 24, 2018May 24, 2018