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We explore model-based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the(More)
It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous(More)
We derive group branching laws for formal characters of subgroups Hπ of GL(n) leaving invariant an arbitrary tensor T π of Young symmetry type π where π is an integer partition. The branchings GL(n) ↓ GL(n − 1) , GL(n) ↓ O(n) and GL(2n) ↓ Sp(2n) fixing a vector vi , a symmetric tensor gij = gji and an antisymmetric tensor fij = −fji , respectively, are(More)
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we give an explicit construction of the full set of representations and describe their properties. We apply these results(More)
Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured by demanding that the set of rate-matrices belonging to the model class form a Lie algebra. It is the case that some well-known Markov(More)
The supersymmetric model of 1] for the evolution of the genetic code is elaborated. Energy considerations in nucleic acid strand modelling, using sl(2) polarity spin and sl(2=1) family box quartet symmetry, lead for the case of codons and anticodons to assignments of codons to 64-dimensional sl(6=1) ' A(5; 0) multiplets. In a previous paper 1] we(More)