Hands-on tutorials for common population- and conservation-genomics analyses, written for students and collaborators working with non-model / wildlife whole-genome data. Worked examples use Neotropical wildlife (e.g. Neofelis) as case studies.
| File | Topic |
|---|---|
Heterozigosity_angsd tutorial.md |
Per-individual heterozygosity from BAMs with ANGSD (SAF → realSFS), suitable for low-coverage data |
PSMC tutorial.md |
Reconstructing historical effective population size with the PSMC coalescent model |
SNP density tutorial.md |
Computing and interpreting SNP density along the genome |
Neofelis_snpdenPlot_chr.R |
R: SNP-density plot by chromosome |
Neofelis_snpdenPlot_sample.R |
R: SNP-density plot by sample |
StringDB.md |
Building protein–protein interaction networks with the STRING database |
Each .md file is a self-contained walkthrough — open it and follow along. The R scripts
are run with Rscript <script>.R and will install the CRAN packages they need on first run.
- popgen-scripts — standalone, parameterized versions of several of these analyses as reusable command-line tools.
- Congen2025 — the full Conservation Genomics Workshop curriculum these tutorials feed into.