Fig. 1

Overview of the fagin pipeline. Inputs (yellow rhombuses) are passed into fagin; the syntenic search intervals on the target genome corresponding to each query gene are delineated using synder [40]. The fagin pipeline consists of three stages. Stage 1: all input is validated, summarized, and secondary data (protein sequences, transcripts, ORFs) are extracted from genomes. Stage 2: The search intervals in the genomes of the target species that correspond to each query genes are searched to determine whether there is homology to the amino acid sequence (AAic) or nucleotide sequence (NTic) of that query gene, and if so where the homology occurs. Alternately, no homology might be detected (unknown). Stage 3: For each query gene, the homology classes are compared across the phylogenetic tree to infer that gene’s history. Fagin is customizable by the user. Output (red rhombuses) can include, e.g., summaries of the transformed input data, homology classes for each query gene against each target genome with statistical designations, and summaries of the homology results for each query gene across all genomes