Related papers: Algorithms for the Majority Rule (+) Consensus Tre…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
This paper introduces the Cartesian Merkle Tree, a deterministic data structure that combines the properties of a Binary Search Tree, a Heap, and a Merkle tree. The Cartesian Merkle Tree supports insertions, updates, and removals of…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Inspired by [4] we present a new algorithm for uniformly random generation of ordered trees in which all occuring outdegrees can be specified by a given sequence of numbers. The method can be used for random generation of binary or n-ary…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
The k-Tree algorithm [Wagner 02] is a non-trivial algorithm for the average-case k-SUM problem that has found widespread use in cryptanalysis. Its input consists of k lists, each containing n integers from a range of size m. Wagner's…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
We present a $\lg n + 2 \lg \lg n+3$ ancestry labeling scheme for trees. The problem was first presented by Kannan et al. [STOC 88'] along with a simple $2 \lg n$ solution. Motivated by applications to XML files, the label size was improved…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
We give an $m^{1+o(1)}\beta^{o(1)}$-time algorithm for generating a uniformly random spanning tree in an undirected, weighted graph with max-to-min weight ratio $\beta$. We also give an $m^{1+o(1)}\epsilon^{-o(1)}$-time algorithm for…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
The sorting problem is one of the most relevant problems in computer science. Within the scope of modern computer science it has been studied for more than 70 years. In spite of these facts, new sorting algorithms have been developed in…
We consider distributed plurality consensus in a complete graph of size $n$ with $k$ initial opinions. We design an efficient and simple protocol in the asynchronous communication model that ensures that all nodes eventually agree on the…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
We use a cluster ensemble to determine the number of clusters, k, in a group of data. A consensus similarity matrix is formed from the ensemble using multiple algorithms and several values for k. A random walk is induced on the graph…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…