Phylogenetic mixtures and linear invariants for equal input models

The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies becoming indistinguishable from the data, even for infinitely long sequences. However, when the underlying Markov process supports linear phylogenetic invariants, then provided these are sufficiently informative, the identifiability of the tree topology can be restored. In this paper, we investigate a class of processes that support linear invariants once the stationary distribution is fixed, the ‘equal input model’. This model generalizes the ‘Felsenstein 1981’ model (and thereby the Jukes–Cantor model) from four states to an arbitrary number of states (finite or infinite), and it can also be described by a ‘random cluster’ process. We describe the structure and dimension of the vector spaces of phylogenetic mixtures and of linear invariants for any fixed phylogenetic tree (and for all trees—the so called ‘model invariants’), on any number n of leaves. We also provide a precise description of the space of mixtures and linear invariants for the special case of n=4 leaves. By combining techniques from discrete random processes and (multi-) linear algebra, our results build on a classic result that was first established by James Lake (Mol Biol Evol 4:167–191, 1987).Peer ReviewedPostprint (author's final draft

Spectral Properties of Quantum Walks on Rooted Binary Trees

We define coined Quantum Walks on the infinite rooted binary tree given by unitary operators $U(C)$ on an associated infinite dimensional Hilbert space, depending on a unitary coin matrix $C\in U(3)$, and study their spectral properties. For circulant unitary coin matrices $C$, we derive an equation for the Carath\'eodory function associated to the spectral measure of a cyclic vector for $U(C)$. This allows us to show that for all circulant unitary coin matrices, the spectrum of the Quantum Walk has no singular continuous component. Furthermore, for coin matrices $C$ which are orthogonal circulant matrices, we show that the spectrum of the Quantum Walk is absolutely continuous, except for four coin matrices for which the spectrum of $U(C)$ is pure point

Parallel Construction of Wavelet Trees on Multicore Architectures

The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their construction time. In this paper, we introduce two algorithms that reduce the time complexity of a wavelet tree's construction by taking advantage of nowadays ubiquitous multicore machines. Our first algorithm constructs all the levels of the wavelet in parallel in $O(n)$ time and $O(n\lg\sigma + \sigma\lg n)$ bits of working space, where $n$ is the size of the input sequence and $\sigma$ is the size of the alphabet. Our second algorithm constructs the wavelet tree in a domain-decomposition fashion, using our first algorithm in each segment, reaching $O(\lg n)$ time and $O(n\lg\sigma + p\sigma\lg n/\lg\sigma)$ bits of extra space, where $p$ is the number of available cores. Both algorithms are practical and report good speedup for large real datasets.Comment: This research has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sk{\l}odowska-Curie Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094

Commutative combinatorial Hopf algebras

We propose several constructions of commutative or cocommutative Hopf algebras based on various combinatorial structures, and investigate the relations between them. A commutative Hopf algebra of permutations is obtained by a general construction based on graphs, and its non-commutative dual is realized in three different ways, in particular as the Grossman-Larson algebra of heap ordered trees. Extensions to endofunctions, parking functions, set compositions, set partitions, planar binary trees and rooted forests are discussed. Finally, we introduce one-parameter families interpolating between different structures constructed on the same combinatorial objects.Comment: 29 pages, LaTEX; expanded and updated version of math.CO/050245

The Combinatorics of Iterated Loop Spaces

It is well known since Stasheff's work that 1-fold loop spaces can be described in terms of the existence of higher homotopies for associativity (coherence conditions) or equivalently as algebras of contractible non-symmetric operads. The combinatorics of these higher homotopies is well understood and is extremely useful. For $n \ge 2$ the theory of symmetric operads encapsulated the corresponding higher homotopies, yet hid the combinatorics and it has remain a mystery for almost 40 years. However, the recent developments in many fields ranging from algebraic topology and algebraic geometry to mathematical physics and category theory show that this combinatorics in higher dimensions will be even more important than the one dimensional case. In this paper we are going to show that there exists a conceptual way to make these combinatorics explicit using the so called higher nonsymmetric $n$-operads.Comment: 23 page

Hopf Algebras of m-permutations, (m+1)-ary trees, and m-parking functions

The m-Tamari lattice of F. Bergeron is an analogue of the clasical Tamari order defined on objects counted by Fuss-Catalan numbers, such as m-Dyck paths or (m+1)-ary trees. On another hand, the Tamari order is related to the product in the Loday-Ronco Hopf algebra of planar binary trees. We introduce new combinatorial Hopf algebras based on (m+1)-ary trees, whose structure is described by the m-Tamari lattices. In the same way as planar binary trees can be interpreted as sylvester classes of permutations, we obtain (m+1)-ary trees as sylvester classes of what we call m-permutations. These objects are no longer in bijection with decreasing (m+1)-ary trees, and a finer congruence, called metasylvester, allows us to build Hopf algebras based on these decreasing trees. At the opposite, a coarser congruence, called hyposylvester, leads to Hopf algebras of graded dimensions (m+1)^{n-1}, generalizing noncommutative symmetric functions and quasi-symmetric functions in a natural way. Finally, the algebras of packed words and parking functions also admit such m-analogues, and we present their subalgebras and quotients induced by the various congruences.Comment: 51 page