Tarantula Species Barcoding & Phylogenetics (R)
Beginner R bioinformatics: COI DNA barcoding, alignment, genetic distances, and phylogenetics for tarantula species.
Uses mitochondrial COI barcode sequences to compare look-alike tarantula species, quantify genetic distance, and visualize relatedness with a neighbor-joining tree in R.
An R bioinformatics pipeline that pulls COI DNA barcodes for closely related tarantula species, aligns sequences, computes pairwise genetic distances, and builds a neighbor-joining phylogenetic tree to test whether species that look similar are actually closely related.
Uses mitochondrial COI barcode sequences to compare look-alike tarantula species, quantify genetic distance, and visualize relatedness with a neighbor-joining tree in R. Public FASTA data comes from NCBI GenBank and BOLD Systems.
Pipeline steps
- Load sequences — read FASTA with Biostrings::readDNAStringSet()
- Align — multiple sequence alignment with msa::msa()
- Distance matrix — pairwise genetic distances via ape::dist.dna(), export CSV
- Tree — neighbor-joining with ape::nj(); plot with plot.phylo() or ggtree
- Interpret — compare genetic vs. morphological similarity across species
- Outputs — distance matrix (CSV) and phylogenetic tree plot (PNG)
Tech stack
- Language — R
- Packages — ape, Biostrings, msa, ggtree (optional), BiocManager
- Data — FASTA from NCBI GenBank / BOLD Systems
- Methods — DNA barcoding (COI), MSA, pairwise genetic distances, neighbor-joining phylogenetics