Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries
Calculate paleo diversity curves through different methods
Find and fix small rounding errors in ultrametric trees
Counting protein sequence differences
Estimate speciation assuming a pure-birth process
Fit a constant-rate birth-death process to a phylogeny
Make a lineage through time (LTT) plot
Simulating natural selection through time in a bi-allelic gene
Simulating one generation of genotypes under Hardy-Weinberg equilibriu...
Plot NatSelSim output
Plotting the whale phylogeny and coloring its clades
Plot protein sequence(s)
Plot a literal interpretation of a fossil record
Plot WFDriftSim output
Details, generics, and methods for the ProteinSeq class
Simulating richness through birth-death processes
Simulating a phylogenetic trees through the birth-death process
Simulating generations of genetic drift in a Wright–Fisher (WF) popula...
"Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.