1 Terrace Aware Phylogenomic Inference from Supermatrices Olga Chernomor 1,2 , Arndt von Haeseler 1,2 and Bui Quang Minh 1 1 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medi- cal University of Vienna, A-1030 Vienna, Austria. 2 Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, A- 1090 Vienna, Austria. Corresponding author: Bui Quang Minh Center for Integrative Bioinformatics Vienna (CIBIV) Max F. Perutz Laboratories Dr. Bohrgasse 9 A-1030 Vienna, Austria Tel: 0043 1 4277 24007 Fax: 0043 1 4277 24098 Email: minh.bui@univie.ac.at Keywords: phylogenetic terraces, maximum likelihood, partition models Abbreviations: ML – Maximum Likelihood, PTA - phylogenetic terrace aware, NNI - nearest neighbor interchange, AA – amino acid. Running head: Terrace aware phylogenomic inference from supermatrices Abstract One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, the resulting so-called supermatrix is usually sparse, that is, not every gene sequence is available for all species in the supermatrix. Due to the missing sequence in- formation a phylogenetic inference, assuming that each gene evolves with its own substitution model, suffers from phylogenetic terraces on which many phylogenetic trees show the same likelihood. Here,