Roland Wittler | Searcharxiv

arXiv2019

Alignment- and reference-free phylogenomics with colored de-Bruijn graphs

We present a new whole-genome based approach to infer large-scale phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de-Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.

q-bio.PE↗

arXiv2017

Fast and Simple Jumbled Indexing for Binary RLE Strings

Important papers have appeared recently on the problem of indexing binary strings for jumbled pattern matching, and further lowering the time bounds in terms of the input size would now be a breakthrough with broad implications. We can still make progress on the problem, however, by considering other natural parameters. Badkobeh et al.\ (IPL, 2013) and Amir et al.\ (TCS, 2016) gave algorithms that index a binary string in $O (n + ρ^2 \log ρ)$ time, where $n$ is the length and $ρ$ is the number of runs, and Giaquinta and Grabowski (IPL, 2013) gave one that runs in $O (n + ρ^2)$ time. In this paper we propose a new and very simple algorithm that also runs in $O(n + ρ^2)$ time and can be extended either so that the index returns the position of a match (if there is one), or so that the algorithm uses only $O (n)$ bits of space.

cs.DS↗

arXiv2016

The SCJ small parsimony problem for weighted gene adjacencies (Extended version)

Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies, and either try to reconstruct all ancestral genomes under a global evolutionary parsimony criterion, or, focusing on a single ancestral genome, use a scaffolding approach to select a subset of ancestral gene adjacencies, generally aiming at reducing the fragmentation of the reconstructed ancestral genome. In this paper, we describe an exact algorithm for the Small Parsimony Problem that combines both approaches. We consider that gene adjacencies at internal nodes of the species phylogeny are weighted, and we introduce an objective function defined as a convex combination of these weights and the evolutionary cost under the Single-Cut-or-Join (SCJ) model. The weights of ancestral gene adjacencies can e.g. be obtained through the recent availability of ancient DNA sequencing data, which provide a direct hint at the genome structure of the considered ancestor, or through probabilistic analysis of gene adjacencies evolution. We show the NP-hardness of our problem variant and propose a Fixed-Parameter Tractable algorithm based on the Sankoff-Rousseau dynamic programming algorithm that also allows to sample co-optimal solutions. We apply our approach to mammalian and bacterial data providing different degrees of complexity. We show that including adjacency weights in the objective has a significant impact in reducing the fragmentation of the reconstructed ancestral gene orders.

cs.DS↗