摘要Bi-directional BLAST is a simple approach to detect,annotate,and analyze candidate orthologous or paralogous sequences in a single go.This procedure is usually confined to the realm of customized Perl scripts,usually tuned for UNIX-like environments.Porting those scripts to other operating systems involves refactoring them,and also the installation of the Perl programming environment with the required libraries.To overcome these limitations,a data pipeline was implemented in Java.This application submits two batches of sequences to local versions of the NCBI BLAST tool,manages result lists,and refines both bi-directional and simple hits.GO Slim terms are attached to hits,several statistics are derived,and molecular evolution rates are estimated through PAML.The results are written to a set of delimited text tables intended for further analysis.The provided graphic user interface allows a friendly interaction with this application,which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/under the GNU GPL license.