Jarvis, P. D. and J. G. Sumner (2013). Matrix group structure and Markov in- variants in the strand symmetric phylogenetic substitution model. arXiv preprint arXiv:1307.5574. Jayaswal, V., F. Ababneh, L. S. Jermiin, and J. Robinson (2011). Reducing model complexity of the general Markov model of evolution. Molecular Biology and Evolution 28(11), 3045–3059. Jayaswal, V., T. K. Wong, J. Robinson, L. Poladian, and L. S. Jermiin (2014). Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages. Systematic Biology 63(5), 726–742. Kaehler, B. D., V. B. Yap, R. Zhang, and G. A. Huttley (2015). Genetic distance for a general non-stationary Markov substitution process. Systematic Biology 64(2), 281–293. Knight, R., P. Maxwell, A. Birmingham, J. Carnes, J. G. Caporaso, B. C. Easton, M. Eaton, M. Hamady, H. Lindsay, Z. Liu, C. Lozupone, D. McDonald, M. Robe- son, R. Sammut, S. Smit, M. J. Wakefield, J. Widmann, S. Wikman, S. Wilson, H. Ying, and G. A. Huttley (2007). PyCogent: a toolkit for making sense from sequence. Genome Biology 8(8), R171. Lake, J. A. (1994). Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proceedings of the National Academy of Sciences 91(4), 1455–1459. Lobry, J. (1995). Properties of a general model of DNA evolution under no-strand- bias conditions. Journal of Molecular Evolution 40(3), 326–330. Lobry, J. and C. Lobry (1999). Evolution of DNA base composition under no-strand- 27