Resources
Software, datasets, teaching materials, and tools produced by our lab.
Software
- chromePlus Markov models for chromosome + binary trait evolution — guide · history
- evobiR Analysis, simulation & teaching functions — vignette
- SAGA2 Model-averaged line cross analysis (AICc)
- DirectRepeateR Direct repeat annotation in genome assemblies
- TraitTrawler Automated trait data collection from the literature
- micRocounter Fast 2–6mer repeat identification
- All GitHub repos →
- Population Genetics Simulator Wright-Fisher: drift, selection, mutation, migration, sex chromosomes
- Birth-Death Tree Simulator Same rates, different outcomes — stochasticity of macroevolution
- CaveCrawler Interactive cave fish (Astyanax) bioinformatics
- Phylogenetic Tree Explorer Interactive tree viewer: load Newick, explore traits, multiple layouts
- AI Tools for Biologists Curated tools for data-driven biology
- Research Glossary PCM, chromosome evolution, and pop-gen terms defined
Data
- Karyotype Databases 14,000+ cytogenetic records — beetles, flies, amphibians, mammals, Polyneoptera
- Circadian Period (τ) Database 1,634 free-running period measurements across the tree of life
- Tree of Sex Database 30,000+ records on sex determination across the tree of life
- Public Data Sources AVONET, PanTHERIA, GBIF, Open Tree of Life, Dryad & more
- History of Chromosome Evolution Stebbins to ChromEvol — a century of ideas
- How Sex Chromosomes Evolve Visual guide — from autosomes to X, Y, Z, W and beyond
- Evolution of Genome Structure Fusions, fissions, polyploidy, and karyotype stasis vs. lability
- Publication Network Interactive co-authorship graph
- Graduate Funding Opportunities
- TA Assignment App Tutorial · Google Form
- Raspberry Pi Cluster Build 26-node Pi 4B cluster notes
Teaching
- Phylogenetic Comparative Methods Interactive guide: phylogenies → continuous → discrete → combined
- Phylogenetics 101 3-hour intro for upper undergrads / early grad students
- R for Biologists Tutorials for common ecology & evolution analyses; no prior R needed
- Experimental Design Statistically tractable experiment design using R
- CURE Data Guide Undergrad research: chromosome number evolution
- BIOL 682: Communication in Bio Sci Scientific writing, storytelling, peer review & revision
- Foundations of Evo Bio Seminar — foundational papers of the modern synthesis
- Fall 2025 Journal Club JEB 2024 reading list
- Grad School Orientation Mentoring, identity, and securing jobs
- Foundational Resources Data, writing, and career planning tools
- AI Prompting Guide Paper review, qual exam simulation, and more