Benchmark details. The colors yellow, red and green point to genes from different COGs. Exact color matches indicate genes within the same LOFTyCOG cluster, presumably true orthologs. a. Possible outcomes. Gene g0 from species S0 is selected for analysis. Its gene neighborhood are genes in LOFT cluster Lb and La. In all cases, there is exactly one gene with gene order conservation. b. Excluded cases. Species S1 is excluded from the benchmark becauseg there are two genes with gene-order conservation; the first conserves La, the second conserves Lb. Species S2 is excluded from the benchmark because there is no strict gene-order conservation due to different directions of transcription. Species S3 is excluded from the benchmark because it has only one gene in C0; there is no possibility for ambiguity in its selection.