Fig. 2

GriffinDetector pipeline flowchart. The light blue ovals indicate the data input or final output data, the green diamonds indicate the thresholds used, the purple cylinders indicate the data generated, and the red boxes indicate data processing. A, F Whether the gene is present in the species /group or not. B, C All the species are categorized into three groups according to their phylogeny: species in the out-group are fixed based on the control file (red dashed box) while the other two groups are dynamic (green and yellow dashed box); the focus species is the initial species in the in-group, then, the closest node or clade will be added into the in-group gradually; the remaining species belong to the mid-group; the process will be stop when only one species remains in the mid-group. D, E When the species belonging to the three groups are clear, BLASTP hits from the focus species query gene are categorized into long hit copies or short hit copies for each species: hits having more than 80% sequence coverage of the query gene are recorded as long copies (line d); the remaining longest hits which have no overlap with each other indicate short copies (lines b and c); other hits (lines a_i) are ignored