Pipeline for Biodiversity Assessment using GenBank data
Copyright © 2013 Anna Papadopoulou, Douglas Chesters & Jesús
of Perl scripts to automate taxonomic assignment of DNA sequences based on
phylogenetic analyses using homologous data obtained from GenBank and,
optionally, a custom local reference database. The method was
originally designed to identify angiosperm species based on psbA-trnH sequences, but it can be
easily adapted to any taxonomic group and marker.
Download the software here.
BAGpipe comes with a very detailed manual.
Web-based implementation of BAGpipe here: <currently under
The explanation of the method is available in:
Papadopoulou, A., Chesters, D., Coronado, I., De la Cadena, G.,
Cardoso, A., Reyes, J.C., Maes, J.-M., Rueda, R.M. & Gómez-Zurita,
J. 2015. Automated DNA-based plant identification for large-scale
biodiversity assessment. Mol. Ecol. Res. 15: 136-152.