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Abstract
Phyloinformatics is an interdisciplinary study, combining Phylogenetics and Informatics. Itinvolves gathering, storing, computing, and reusing the product of phylogenetic analyses.One of the major challenges in the domain of phylogenetics is the accessibility of publishedphylogenetic trees and the data that are used to estimate these trees. With the helpof Semantic Web technology, we can make phylogenetic resources more understandable tothe web agents and facilitate the reusability of accessible phylogentic trees and associatedmetadata. This thesis presents an ontology-driven, semantic problem-solving environmentfor phylogenetic analysis, including four research efforts to achieve this goal. PhylOnt, asan ontology for phylogenetic analysis. PhylAnt-D and PhylAnt-X, to annotate phylogeneticdocuments and NeXML files. Finally, MUDDIS as a MUlti-Dimentional semantic integrativeapproach for knowledge DIScovery to reconstruct the gene tree based on differentgene similarities. The outcome of this research is to advanced phyloinformatics to reusedata sources in phylogenetic analysis with the help of Semantic Web technologies.