Gómez-Zurita Lab
Herbivore Beetle Evolution
Animal Biodiversity and Evolution Programme
Institut de Biologia Evolutiva (CSIC-UPF)
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Software

bfca: Bayes Factor Cluster Analysis

Copyright © 2012 Carmelo Andújar, Víctor Soria-Carrasco & Jesús Gómez-Zurita

Suite of R scripts to evaluate statistical congruence among molecular clock calibration points by quantifying the changes in marginal likelihoods of trees from sequentially constrained Bayesian inference analyses using Bayes Factors.

Download BFCA 1.0.2 here: Linux (source code), Mac OS X, Windows 7.
For installation and details, visit Dr. Soria-Carrasco Bitbucket wiki.

The explanation of the method is available in:
Andújar, C., Soria-Carrasco, V., Serrano, J. & Gómez-Zurita, J. 2014. Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons. Methods Ecol. Evol. 5: 226-242.


BAGpipe: Pipeline for Biodiversity Assessment using GenBank data

Copyright © 2013 Anna Papadopoulou, Douglas Chesters & Jesús Gómez-Zurita

Suite 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 construction>.

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.