1. Phylogenomic supertrees: the end of the road or the light at the end of the tunnel? Olaf R. P. Bininda-Emonds Friedrich-Schiller-Universität Jena

4. Formal supertree construction A B D C E I J F G H K L E J F G H K L A B C K L D C E I H K Agreement Optimization consensus-like techniques coding technique optimization criterion

5. “ Traditional” supertrees

18. Archimedean phylogenetics “ Give me a cluster large enough and a data set on which to work on, and I shall derive the phylogeny.”

20. BUILD MR / O Global optimization Supertree construction Subtree optimization Divide Accuracy Speed Stage n/a

21. subsample data (4, 8, 16, …, 1024, 2048 taxa) simulate data (K2P, ti:tv = 2.0,  = 0.5,  = 0.1, 2000 bp) phylogenetic analysis (NJ, weighted MP, ML, or ML-DCM3) compare to pruned model tree

23. BUILD MR / O Global optimization Supertree construction Subtree optimization Divide Accuracy Speed Stage n/a

29. BUILD MR / O Global optimization Supertree construction Subtree optimization Divide Accuracy Speed Stage n/a

42. Bicliques A B D F C G E Taxa Genes 6 3 4 1 7 5 8 2 1 2 3 4 5 6 7 8 A + – – – – – – – B + + – – – – – – C – + + + + – – – D – + + + + + – – E – + + + + – – – F – – – – – + + – G – – – – – – + + Taxa Genes maximal biclique = K 4,3