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EUCALYPT: efficient tree reconciliation enumerator

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Pareto-optimal phylogenetic tree reconciliation

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Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

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(2012) Maureen Stolzer et al.   BIOINFORMATICS

Wolbachia detection: an assessment of standard PCR Protocols

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Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

A parameter-adaptive dynamic programming approach for inferring cophylogenies

(2010) Daniel Merkle et al.   BMC BIOINFORMATICS

Simultaneous Identification of Duplications and Lateral Gene Transfers

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The Cophylogeny Reconstruction Problem Is NP-Complete

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Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE