Calculating the nonparametric statistical metrics to assess the extent of DNA barcode gap overlap/separation
To perform the analysis:
- Place folder containing the DNA sequence alignments in Desktop. Users should ensure their own data closely follows this format.
- 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. - Run
barcode_clean.R
to calculate the metrics. A pop-up window will appear to select a FASTA file. - Run
summary_stats.R
to generate summary statistics for the metrics. - Run
bootstrap_coalescent.R
to perform nonparametric bootstrapping to calculate 95% confidence intervals.
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.