Evolving Phylogenetic Trees: an Alternative to Black-Box Approaches
نویسندگان
چکیده
This paper presents the main steps to reconstruct phylogenetic trees using an evolutionary algorithm with a wide range of alternative computational procedures for fitness evaluation and for tuning the search engine. Due to the fine equilibrium between exploration and exploitation of the search space, highquality reconstructions are obtained among an explosion of candidates and with the additional requirement of adjusting the length of all branches in a given tree. A toolbox is available, and the matrix codification adopted, the associated genetic operators, and the optimization procedures involved are clearly described to guarantee reproducibility.
منابع مشابه
Rainfall-runoff modelling using artificial neural networks (ANNs): modelling and understanding
In recent years, artificial neural networks (ANNs) have become one of the most promising tools in order to model complex hydrological processes such as the rainfall-runoff process. In many studies, ANNs have demonstrated superior results compared to alternative methods. ANNs are able to map underlying relationship between input and output data without prior understanding of the process under in...
متن کاملKnowledge Extraction from the Neural ‘Black Box’ in Ecological Monitoring
Phytoplankton biomass within the Saginaw Bay ecosystem (Lake Huron, Michigan, USA) was characterized as a function of select physical/chemical indicators. The complexity and variability of ecological systems typically make it difficult to model the influences of anthropogenic stressors and/or natural disturbances. Here, Artificial Neural Networks (ANNs) were developed to model chlorophyll a con...
متن کاملEstimating phylogenetic trees from genome-scale data.
The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a...
متن کاملA Hybrid Diagnosis Approach Combining Black-Box and White-Box Reasoning
We study model-based diagnosis and propose a new approach of hybrid diagnosis combining black-box and white-box reasoning. We implemented and compared different diagnosis approaches including the standard hitting set algorithm and new approaches using answer set programming engines (DLV, Potassco) in the application of EULER/X toolkit, a logic-based toolkit for alignment of multiple biological ...
متن کاملBlack-box Testing for Evolving COTS-Based Software
Black-box testing methods are widely used in system level and integration testing. But in the context of COTS-based engineering, when newly modified COTS components are adopted into the system and the source code is not available, black-box testing is a necessary and feasible approach to assure that these COTS products do not adversely affect the software. In this paper, we first discuss challe...
متن کامل