DNA-Barcode-Gap-Coalescent

Calculating the nonparametric statistical metrics to assess the extent of DNA barcode gap overlap/separation

How to Run

To perform the analysis:

1. Place folder containing the DNA sequence alignments in Desktop. Users should ensure their own data closely follows this format.
2. Run load.R to set parameters. Users can alter the employed distance model, dist_model, as well as the employed amino acid codon table, AA_code as needed for their own marker-specific datasets.
3. Run barcode_clean.R to calculate the metrics. A pop-up window will appear to select a FASTA file.
4. Run summary_stats.R to generate summary statistics for the metrics.
5. Run bootstrap_coalescent.R to perform nonparametric bootstrapping to calculate 95% confidence intervals.

References

Phillips, J.D., Griswold, C.K., Young, R.G., Hubert, N. and Hanner, R.H. (To appear). A measure of the DNA barcode gap for applied and basic research. Methods in Molecular Biology. Springer.