phyletica

Phyletica Lab: Exploring biodiversification

Auburn, AL

Pinned Repositories

abc-glm-marginal-test
Simulation-based test of general linear model marginal likelihood method
Language:Shell1 2 00
animating-sea-level-change
Shell and R code to create animated gif of sea level change.
Language:R1 2 00
bayes-demo
A demonstration of Bayesian statistics
Language:Python1 5 01
ecoevolity
Estimating evolutionary coevality
Language:C++8 3 02
ecoevolity-model-prior
Analyses exploring the behavior of new comparative biogeographical model priors.
Language:Shell1 5 00
ecoevolity-one-locus-experiments
Simulation-based experiments to assess how ecoevolity handles single-locus datasets.
Language:TeX0 2 00
gekgo
Comparative phylogenetics of Philippine gekkonids
Language:HTML1 2 00
lab-protocols
Laboratory protocols used in the Phyletica Lab at Auburn University
61
pycoevolity
A python package for summarizing the output of Ecoevolity
Language:Python10
SumTimes
Tool for estimating the probability of divergence-time scenarios from posterior samples of trees.
Language:Python1 2 01

phyletica's Repositories

phyletica/ecoevolity
Estimating evolutionary coevality
Language:C++8 3 02
phyletica/lab-protocols
Laboratory protocols used in the Phyletica Lab at Auburn University
61
phyletica/abc-glm-marginal-test
Simulation-based test of general linear model marginal likelihood method
Language:Shell1 2 00
phyletica/animating-sea-level-change
Shell and R code to create animated gif of sea level change.
Language:R1 2 00
phyletica/bayes-demo
A demonstration of Bayesian statistics
Language:Python1 5 01
phyletica/ecoevolity-model-prior
Analyses exploring the behavior of new comparative biogeographical model priors.
Language:Shell1 5 00
phyletica/gekgo
Comparative phylogenetics of Philippine gekkonids
Language:HTML1 2 00
phyletica/pycoevolity
A python package for summarizing the output of Ecoevolity
Language:Python10
phyletica/SumTimes
Tool for estimating the probability of divergence-time scenarios from posterior samples of trees.
Language:Python1 2 01
phyletica/ecoevolity-docker
A repo for building a Docker image running ecoevolity
00
phyletica/ecoevolity-one-locus-experiments
Simulation-based experiments to assess how ecoevolity handles single-locus datasets.
Language:TeX0 2 00
phyletica/weighted-discount-process-notes
Some thoughts on Dirichlet and Pitman-Yor processes and possible extensions of them.
Language:TeX0 2 00
phyletica/apaep-evolution
Materials for teaching evolution for the Alabama Prison Arts + Education Project (APAEP)
Language:TeX2 0
phyletica/bayesian-lizard-flipping
Bayesian probability of flipping lizrds.
Language:Jupyter Notebook
phyletica/codiv-sanger-bake-off
Comparing approximate and full-likelihood approaches to estimating temporal clustering of divergence times among taxa.
Language:Shell
phyletica/codiv-sanger-bake-off-tex
TeX files for the Phyletica Lab project at http://phyletica.org/codiv-sanger-bake-off
Language:TeX
phyletica/ecoevolity-demog-experiments
Simulation experiments to explore statistical behavior of estimating shared demographic changes.
Language:TeX1
phyletica/ecoevolity-example-data
Example data for running ecoevolity
2 0
phyletica/ecoevolity-experiments
Analyses exploring the behavior of Ecoevolity, a method for estimating shared evolutionary events.
Language:TeX2 0
phyletica/ecoevolity-model-prior-tex
TeX files for the Phyletica Lab project at http://phyletica.org/ecoevolity-model-prior
Language:TeX5 0
phyletica/ecoevolity-operator-tests
A repo for testing the efficiency of MCMC operators implemented in ecoevolity.
Language:Shell2 0
phyletica/ecoevolity-sumatran-frogs
Simulations to assess performance of ecoevolity conditional on Sumatran frog genomic data.
Language:Python
phyletica/fragcoalsim-web
A web implementation of fragcoalsim
Language:HTML
phyletica/hmmer
HMMER: biological sequence analysis using profile HMMs (fork to report forward and Viterbi scores)
Language:C0 0
phyletica/phycoeval-experiments
Analyses exploring the behavior of generalized Bayesian phylogenetics
Language:R
phyletica/phyletica.github.io
phyletica.github.io
Language:HTML2
phyletica/SDSDsim
Simulating trees under a state-dependent birth-death process with shared and divergences
Language:Python
phyletica/tikz-codivergence-cartoons
LaTeX (tikz) and Bash code for creating animated examples of shared divergences.
Language:TeX2 0