MeDuSa: a multi-draft based scaffolder.

MOTIVATION: Completing the genome sequence of an organism is an important task in comparative, functional and structural genomics. However, this remains a challenging issue from both a computational and an experimental viewpoint. Genome scaffolding (i.e. the process of ordering and orientating contigs) of de novo assemblies usually represents the first step in most genome finishing pipelines. RESULTS: In this article we present MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalizes the scaffolding problem by means of a combinatorial optimization formulation on graphs and implements an efficient constant factor approximation algorithm to solve it. In contrast to currently used scaffolders, it does not require either prior knowledge on the microrganisms dataset under analysis (e.g. their phylogenetic relationships) or the availability of paired end read libraries. This makes usability and running time two additional important features of our method. Moreover, benchmarks and tests on real bacterial datasets showed that MeDuSa is highly accurate and, in most cases, outperforms traditional scaffolders. The possibility to use MeDuSa on eukaryotic datasets has also been evaluated, leading to interesting results.

EUCALYPT: efficient tree reconciliation enumerator.

BACKGROUND: Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tree using event-based maximum parsimony. Given a cost model for the events, many optimal reconciliations are however possible. Any further biological interpretation of them must therefore take this into account, making the capacity to enumerate all optimal solutions a crucial point. Only two algorithms currently exist that attempt such enumeration; in one case not all possible solutions are produced while in the other not all cost vectors are currently handled. The objective of this paper is two-fold. The first is to fill this gap, and the second is to test whether the number of solutions generally observed can be an issue in terms of interpretation. RESULTS: We present a polynomial-delay algorithm for enumerating all optimal reconciliations. We show that in general many solutions exist. We give an example where, for two pairs of host-parasite trees having each less than 41 leaves, the number of solutions is 5120, even when only time-feasible ones are kept. To facilitate their interpretation, those solutions are also classified in terms of how many of each event they contain. The number of different classes of solutions may thus be notably smaller than the number of solutions, yet they may remain high enough, in particular for the cases where losses have cost 0. In fact, depending on the cost vector, both numbers of solutions and of classes thereof may increase considerably. To further deal with this problem, we introduce and analyse a restricted version where host switches are allowed to happen only between species that are within some fixed distance along the host tree. This restriction allows us to reduce the number of time-feasible solutions while preserving the same optimal cost, as well as to find time-feasible solutions with a cost close to the optimal in the cases where no time-feasible solution is found. CONCLUSIONS: We present Eucalypt, a polynomial-delay algorithm for enumerating all optimal reconciliations which is freely available at http://eucalypt.gforge.inria.fr/.