Additional file 2: of Benchmarking of alignment-free sequence comparison methods

Figure S1. Comparison (tanglement) of test tree and reference tree of sulfatase modifying factor (SUMF) gene family in Eukaryotes. The test tree is inferred by 4 alignment-free measures in AFKS program (mismatch, markov, rre_k_r, kl_conditional). Reference phylogenetic tree was taken from SwissTree. Figure S2. Comparison (tanglement) of test tree and reference tree of complete mitochondrial genomes from 25 labroid fishes. The test tree is inferred by 9 alignment-free programs (AFKS, alfpy, CAFE, FSWM, jD2Stat, kmacs, mash, RTD-Phylogeny, and spaced). Reference phylogenetic tree was taken from [1]. Figure S3. Comparison (tanglement) of test and reference cladograms of complete genomes from 29 E. coli/Shigella species. Test tree was inferred by phylonium. Figure S4. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by co-phylog. Figure S5. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by mash. Figure S6. Comparison (tanglement) of test and reference cladograms of complete genomes from 14 plant species. Test tree was inferred by Multi-SpaM. Figure S7. Comparison (tanglement) of test and reference cladograms of complete genomes from 27 E.coli and Shigella species. Test tree was inferred by andi and co-phylog. Reference phylogenetic tree was constructed in [2–4] from 5282 Bayesian protein trees. E. coli reference groups and Shigella (S) are indicated. Figure S8. Comparison (tanglement) of test and reference cladograms of complete genomes from 27 E. coli and Shigella species. Test tree was inferred by phylonium. Reference phylogenetic tree was constructed in [2–4] from 5282 Bayesian protein trees. E. coli reference groups and Shigella (S) are indicated. Figure S9. Performance scores obtained by alfpy--canberra (dark gray) and AFKS--canberra (light gray) run on common word lengths across data sets. (PDF 1718 kb)