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The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes grass symbionts in the epichloae clade (Epichloë and Neotyphodium species), which are extraordinarily diverse both in their host interactions and in their alkaloid profiles. Epichloae produce alkaloids(More)
Answer-set programming (ASP) solvers must handle difficult computational problems that are NP-hard. These solvers are in the worst case exponential and their scope of applicability, despite recent impressive gains in performance, remains limited. One way to deal with limitations of answer-set programming is to exploit parallelism. In this paper, we design(More)
Image-based electronic editions enable researchers to view and study in an electronic environ­ ment historical manuscript images intricately linked to edition, transcript, glossary and apparatus files. Building image-based electronic editions poses a twofold chal­ lenge. For humanities scholars, it is important to be able to use image and text to(More)
The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family(More)
We demonstrate the Edition Production Technology (EPT), an integrated development environment for building Image-based Electronic Editions (IBEE). EPT is developed in Java on top of Eclipse platform and benefits from the openness of Eclipse's plugin architecture and its portability (currently EPT runs on Windows XP, Linux, and Mac OS X). EPT provides(More)
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by two input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting(More)
Maximum likelihood pedigree reconstruction using integer programming. Preface Computation has become an indispensable method for today's bio-sciences. Many routine tasks of biological research are performed using well-established algorithms. However, the increasing complexity of studied systems demands for new computational solutions to complex and often(More)