A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies

Drinkwater, Benjamin; Charleston, Michael A.

doi:10.1007/978-3-662-48221-6_7

Cited by 2 publications

(2 citation statements)

References 15 publications

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“…traditionally only retains a single mapping site for the parasite leaves (Drinkwater and Charleston 2015a). It is possible, however, to retain multiple mappings for each parasite leaf node, where in fact there is the ability to retain a mapping site for each parasite node to all locations in the host tree, without increasing the asymptotic complexity of the Improved Node Mapping algorithm.…”

Section: Recovering Divergence Eventsmentioning

confidence: 99%

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WiSPA: A new approach for dealing with widespread parasitism

Drinkwater¹,

Qiao²,

Charleston³

2016

Preprint

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Traditionally, studies of coevolving systems have considered cases where a parasite may inhabit only a single host. The case where a parasite may infect many hosts, widespread parasitism, has until recently gained little traction. This is due in part to the computational complexity involved in reconstructing the coevolutionary histories where parasites may infect only a single host, which is NP-Hard. Allowing parasites to inhabit more than one host has been seen to only further compound this computationally intractable problem. Recently however, well-established algorithms for estimating the problem instance where a parasite may infect only a single host have been extended to handle widespread parasites. Although this has offered significant progress, it has been noted that these algorithms poorly handle parasites that inhabit phylogenetically distant hosts.

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Section: Recovering Divergence Eventsmentioning

confidence: 99%

“…This simplified problem, often referred to as the dated tree reconciliation problem (Drinkwater and Charleston 2015a), has been applied within a number of algorithms (Doyon et al 2011;Conow et al 2010;Drinkwater and Charleston 2015b), with the fastest proposed to date running in O(n 2 log n) (Bansal et al 2012).…”

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confidence: 99%

WiSPA: A new approach for dealing with widespread parasitism

Drinkwater¹,

Qiao²,

Charleston³

2016

Preprint

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Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

Drinkwater

Charleston

2016

Algorithms Mol Biol

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BackgroundRecent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogenetic trees. Targeted algorithmic design for specific tree topologies has to date been highly successful, with one recent formulation providing a logarithmic space complexity reduction for the dated tree reconciliation problem.MethodsIn this work we build on this prior analysis providing a further asymptotic space reduction, by providing a new formulation for the dynamic programming table used by a number of popular coevolutionary analysis techniques. This model gives rise to a sub quadratic running time solution for the dated tree reconciliation problem for selected tree topologies, and is shown to be, in practice, the fastest method for solving the dated tree reconciliation problem for expected evolutionary trees. This result is achieved through the analysis of not only the topology of the trees considered for coevolutionary analysis, but also the underlying structure of the dynamic programming algorithms that are traditionally applied to such analysis.ConclusionThe newly inferred theoretical complexity bounds introduced herein are then validated using a combination of synthetic and biological data sets, where the proposed model is shown to provide an space saving, while it is observed to run in half the time compared to the fastest known algorithm for solving the dated tree reconciliation problem. What is even more significant is that the algorithm derived herein is able to guarantee the optimality of its inferred solution, something that algorithms of comparable speed have to date been unable to achieve.

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A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies

Cited by 2 publications

References 15 publications

WiSPA: A new approach for dealing with widespread parasitism

WiSPA: A new approach for dealing with widespread parasitism

Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

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