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In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Given a bipartite graph that has a perfect matching, a prefect proportional allocation is an assignment of positive weights to the nodes of the right partition so that every left node is fractionally assigned to its neighbors in proportion…
In this paper, we revisit the split decomposition of graphs and give new combinatorial and algorithmic results for the class of totally decomposable graphs, also known as the distance hereditary graphs, and for two non-trivial subclasses,…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
We investigate which chordal graphs have a representation as intersection graphs of pseudosegments. For positive we have a construction which shows that all chordal graphs that can be represented as intersection graph of subpaths on a tree…
A T-graph (a special case of a chordal graph) is the intersection graph of connected subtrees of a suitable subdivision of a fixed tree T . We deal with the isomorphism problem for T-graphs which is GI-complete in general - when T is a part…
We introduce a new subclass of chordal graphs that generalizes split graphs, which we call well-partitioned chordal graphs. Split graphs are graphs that admit a partition of the vertex set into cliques that can be arranged in a star…
Let $H$ be a $3$-partite $3$-uniform hypergraph, i.e. a $3$-uniform hypergraph such that every edge intersects every partition class in exactly one vertex, with each partition class of size $n$. We determine a Dirac-type vertex degree…
Recent investigations in computational biology focus on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also be useful for this task. Notably, perfect transfer networks (PTN) explain the character…
Unigraphs are graphs identifiable up to isomorphism from their degree sequences. Given a class $\mathcal{A}$ of graphs, we define the class of $\mathcal{A}$-unigraphs to be graphs identifiable from degree sequence and membership in…
A graph $G=(V,E)$ is a {\it unipolar graph} if there exits a partition $V=V_1 \cup V_2$ such that, $V_1$ is a clique and $V_2$ induces the disjoint union of cliques. The complement-closed class of {\it generalized split graphs} are those…
In this paper, we study the word-representability of well-partitioned chordal graphs using split decomposition. We show that every component of the minimal split decomposition of a well-partitioned chordal graph is a split graph. Thus we…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…