Software & R Packages

• chromePlus Markov models for chromosome + binary trait evolution — guide
• evobiR Analysis, simulation & teaching functions — vignette
• SAGA2 Model-averaged line cross analysis (AICc)
• DirectRepeateR Direct repeat annotation in genome assemblies
• micRocounter Fast 2–6mer repeat identification
• All GitHub repos →

Databases

• Epistasis Database 1,600+ datasets from 130+ papers on the role of epistasis in trait divergence
• 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

Visual Guides

• How Sex Chromosomes Evolve From autosomes to X, Y, Z, W — diagrams, interactive charts, and key papers
• Evolution of Genome Structure Fusions, fissions, polyploidy, meiotic drive, and karyotype stasis
• Epistasis & the Shifting Balance Line cross analysis, SAGA, and the Wright–Fisher debate
• Selection in Evolution Natural, sexual, background, and indirect selection — drift vs. selection
• Coleoptera Genomics Beetle genomes, Stevens elements, dosage compensation, and population genetics
• History of Chromosome Evolution Stebbins to ChromEvol — a century of ideas
• Publication Network Interactive co-authorship graph

Interactive Tools

• Population Genetics Simulator Wright-Fisher: drift, selection, mutation, migration, sex chromosomes
• Birth-Death Tree Simulator Same rates, different outcomes — stochasticity of macroevolution
• Phylogenetic Tree Explorer Load Newick, explore traits, multiple layouts
• CaveCrawler Interactive cave fish (Astyanax) bioinformatics
• Research Glossary PCM, chromosome evolution, and pop-gen terms defined

AI & Automation

• TraitTrawler AI-powered trait data collection from the literature
• AI Tools for Biologists Curated tools for data-driven biology
• AI Prompting Guide Paper review, qual exam simulation, and more
• Karyotype Data Agent Autonomous literature-mining agent for cytogenetic records
• All AI Projects →

Courses & 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
• BIOL 682: Communication in Bio Sci Scientific writing, storytelling, peer review & revision
• CURE Data Guide Undergrad research: chromosome number evolution
• Foundations of Evo Bio Seminar — foundational papers of the modern synthesis
• Fall 2025 Journal Club JEB 2024 reading list

For Graduate Students

• Grad School Orientation Mentoring, identity, and securing jobs
• Graduate Funding Opportunities Fellowships, grants, and funding sources
• Foundational Resources Data, writing, and career planning tools
• Raspberry Pi Cluster Build 26-node Pi 4B cluster notes
• TA Assignment App Tutorial · Google Form