Resources
Curated tools, databases, tutorials, and papers for bioinformatics, genomics, and evolutionary biology. Always growing.
R & Statistics
10Download the RStudio IDE for R development
Comprehensive gallery of R plot types with reproducible code
Lab tutorial: basic statistics and plotting in R (R Markdown)
Lab tutorial: principal component analysis and visualization
Quick code for extracting gene data with taxid information
Tutorial: tree simulation, trait simulation, character mapping
Quick tutorial for time-calibrated phylogenies in R
Very gentle introduction to R for early undergraduates
Introductory guide to data subsetting and filtering
Write-up for annotating phylogenetic trees with data layers
Coding Resources
6Improve coding skills through community code challenges
Online IDE for collaborative and team coding projects
Interactive bioinformatics tutorials in the browser
Learn bioinformatics and programming through problem-solving
Tutorials and references for web coding and scripting
Curated resources and links to help R users transition to Python
Databases
6NIH genetic sequence database — the primary repository for sequence data
Largest public repository of high-throughput sequencing data
Curated genome size data, maintained by T. Ryan Gregory (U. Guelph)
Collections for beetles, Polyneoptera, and amphibians — Blackmon lab, Texas A&M
Sex chromosome systems across many animal lineages
AI-predicted protein structures for nearly every known protein
Useful Websites & Tools
13Online nucleotide and protein sequence identity and alignment
Online multiple sequence alignment for phylogenetics
Real-time pathogen evolution tracking with interactive visualizations
Automated online workflow for building simple phylogenies
Professional science figure and illustration creation
Phylogenetic tools for comparative biology — Liam Revell's R blog
BEAST2 tutorial for Bayesian molecular evolution and phylogenetics
Use lat/long coordinates to identify county for Utah field sites
Free open-source science icons for vector graphics software
Free silhouette images of animals, plants, and other life forms
Faculty and postdoc job listings in ecology and evolution
Online tools for genetics and evolutionary analysis — Duke University
Tools and prototypes for model organism genome data
Useful Programs
4The R statistical computing environment
Bayesian Analysis of Macroevolutionary Mixtures — program and docs
Interactive simulations by Heath Blackmon — Texas A&M
Interactive Brownian motion simulations by Heath Blackmon — Texas A&M
Useful Papers & Articles
6Resources for Drosophilid phylogeny and systematics — GBE
New population genomics resource — MBE
Critical look at software reliability and reproducibility in biology
R package for interactive and reproducible SNP filtering
Guide to browser-based Linux terminals and bash editors
Statistical methods in genetics and zoology courses — CBE Life Sci Ed
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