Flowchart representing the systematic pipeline for the automated detection of horizontal gene transfer in complete genomes. Step 1. Clustering of orthologous groups by OrthoMCL. Step 2. Detection of the presence or absence of genetic events on the species tree and the reconstruction of the phyletic pattern of gene gain and gene loss using PhyloPattern. Step 3. BlastP filter to retrieve the homologous sequences. Step 4. Construction of phylogenetic trees using FIGENIX. Step 5. Detection of HGT events from HGT agent using a transfer filter. Step 6. Validation of HGT cases using Bayesian method. Steps 1 through 5 are included in the pipeline.