819 research outputs found
Algorithms for Visualizing Phylogenetic Networks
We study the problem of visualizing phylogenetic networks, which are
extensions of the Tree of Life in biology. We use a space filling visualization
method, called DAGmaps, in order to obtain clear visualizations using limited
space. In this paper, we restrict our attention to galled trees and galled
networks and present linear time algorithms for visualizing them as DAGmaps.Comment: Appears in the Proceedings of the 24th International Symposium on
Graph Drawing and Network Visualization (GD 2016
Parking functions, labeled trees and DCJ sorting scenarios
In genome rearrangement theory, one of the elusive questions raised in recent
years is the enumeration of rearrangement scenarios between two genomes. This
problem is related to the uniform generation of rearrangement scenarios, and
the derivation of tests of statistical significance of the properties of these
scenarios. Here we give an exact formula for the number of double-cut-and-join
(DCJ) rearrangement scenarios of co-tailed genomes. We also construct effective
bijections between the set of scenarios that sort a cycle and well studied
combinatorial objects such as parking functions and labeled trees.Comment: 12 pages, 3 figure
Boosting Haplotype Inference with Local Search
Abstract. A very challenging problem in the genetics domain is to infer haplotypes from genotypes. This process is expected to identify genes affecting health, disease and response to drugs. One of the approaches to haplotype inference aims to minimise the number of different haplotypes used, and is known as haplotype inference by pure parsimony (HIPP). The HIPP problem is computationally difficult, being NP-hard. Recently, a SAT-based method (SHIPs) has been proposed to solve the HIPP problem. This method iteratively considers an increasing number of haplotypes, starting from an initial lower bound. Hence, one important aspect of SHIPs is the lower bounding procedure, which reduces the number of iterations of the basic algorithm, and also indirectly simplifies the resulting SAT model. This paper describes the use of local search to improve existing lower bounding procedures. The new lower bounding procedure is guaranteed to be as tight as the existing procedures. In practice the new procedure is in most cases considerably tighter, allowing significant improvement of performance on challenging problem instances.
Exact reconciliation of undated trees
Reconciliation methods aim at recovering macro evolutionary events and at
localizing them in the species history, by observing discrepancies between gene
family trees and species trees. In this article we introduce an Integer Linear
Programming (ILP) approach for the NP-hard problem of computing a most
parsimonious time-consistent reconciliation of a gene tree with a species tree
when dating information on speciations is not available. The ILP formulation,
which builds upon the DTL model, returns a most parsimonious reconciliation
ranging over all possible datings of the nodes of the species tree. By studying
its performance on plausible simulated data we conclude that the ILP approach
is significantly faster than a brute force search through the space of all
possible species tree datings. Although the ILP formulation is currently
limited to small trees, we believe that it is an important proof-of-concept
which opens the door to the possibility of developing an exact, parsimony based
approach to dating species trees. The software (ILPEACE) is freely available
for download
Artificial in its own right
Artificial Cells, , Artificial Ecologies, Artificial Intelligence, Bio-Inspired Hardware Systems, Computational Autopoiesis, Computational Biology, Computational Embryology, Computational Evolution, Morphogenesis, Cyborgization, Digital Evolution, Evolvable Hardware, Cyborgs, Mathematical Biology, Nanotechnology, Posthuman, Transhuman
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