PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework.
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Sep 29, 2026 - Python
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macroevolution
Here are 28 public repositories matching this topic...
Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries
phylogenetics population-genetics paleobiology comparative-methods evolutionary-biology macroevolution science-education biodiversity-science simulation-based-learning inquiry-based-learning data-driven-education
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Apr 1, 2026 - R
paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.
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Sep 4, 2026 - R
Bayesian inference of trait evolution under a “fossilized” Brownian motion.
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Jun 1, 2025 - R
A Julia interface to the Paleobiology Database (PBDB) data service.
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Sep 21, 2026 - Julia
Data and analyses used in Moon & Stubbs, Communications Biology doi:10.1038/s42003-020-0779-6
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Feb 17, 2020 - R
Data and code for "The Cultural Macroevolution of Arcade Video Games: Innovation, Collaboration, and Collapse"
research collaboration constraints arcade dataset scaling videogame network-analysis complex-systems cultural-evolution macroevolution
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Nov 4, 2025 - Jupyter Notebook
Data, code & figures used to assess global patterns of potential thermal niche filling
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Sep 21, 2023 - R
Galapagos Islands Testudinidae Macroevolution (GITM)
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May 5, 2025
Benchmarks Physics-Informed Neural ODEs vs. Fine-Tuned Foundation Models (Chronos) on Cenozoic fossil data. Includes a Random Forest analysis of the Lilliput Effect to test climate vs. taphonomy drivers. Results show Neural ODEs outperform generic Transformers (MSE 13.05) in reconstructing deep-time evolutionary history.
bioinformatics deep-learning computational paleoclimate paleontology macroevolution scientific-machine-learning neural-odes chronos-t5 computational-paleobiology
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Dec 14, 2025 - Jupyter Notebook
Paper - A novel function of banded stripes to prevent cannibalism in snake-eating snakes
behaviour herpetology macroevolution ancestral-state-reconstruction ophiophagy serpentes pattern-evolution
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Mar 9, 2022 - R
Interactive 3D phylogenetic tree visualizer for continuous trait evolution and supplied ancestral-state estimates; standalone WebGL2 HTML.
python webgl bioinformatics evolution data-visualization scientific-visualization phylogenetics webgl2 newick interactive-visualization phylogeny 3d-visualization comparative-methods evolutionary-biology phylogenetic-tree macroevolution trait-evolution phylogenetic-visualization continuous-traits ancestral-states
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Sep 30, 2026 - Python
Infer phylogeny parameters with Deep Learning.
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Dec 27, 2022 - Jupyter Notebook
Macroevolutionary analyses of the Monodoreae tribe (Annonaceae) 🧬🌳🌍
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Dec 8, 2023 - R
Supplementary R code for analyses in "Rates of passerine body plan evolution in time and space"
morphology birds phylogenetics spatial-analysis comparative-methods biogeography evolutionary-biology macroevolution passerines
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Jul 28, 2026 - R
R scripts to explore global patterns of diversificatio and species richness of current and present-natural mammals
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Oct 23, 2024 - R
This repository provides research data and source code for reproducing the computational analysis reported in the manuscript "Community-level functional stability in East African herbivores amid major environmental change"
functional-traits macroevolution ecometrics large-herbivorous-mammals faunal-community east-african-rift-system
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Apr 15, 2026 - R
Supplementary code and data for "The paradox of predictability"
time-series-analysis quantitative-genetics phylogenetic-comparative-methods genotype-phenotype-map macroevolution evolvability phenotypic-integration evolutionary-prediction
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Aug 11, 2024 - R
R codes for simulating and detecting punctuated evolution in any clades, from dinosaurs to viruses
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Mar 30, 2024 - R
Paper - Best practices for building and curating databases for comparative analyses
review database open-science biomechanics commentary meta-analysis macroecology ecophysiology macroevolution macrophysiology comparative-physiology
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Mar 15, 2022 - R
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