ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
نویسندگان
چکیده
منابع مشابه
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.
BACKGROUND Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ab...
متن کاملQuantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species
Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...
متن کاملQuantitative Comparison of Tree Pairs Resulted from Gene and Protein Phylogenetic Trees for Sulfite Reductase Flavoprotein Alpha-Component and 5S rRNA and Taxonomic Trees in Selected Bacterial Species
Introduction: FAD is the cofactor of FAD-FR protein family. Sulfite reductase flavoprotein alpha-component is one of the main enzymes of this family. Based on applications of this enzyme in biotechnology and industry, it was chosen as the subject of evolutionary studies in 19 specific species. Method: Gene and protein sequences of sulfite reductase flavoprotein alpha-component, 5S rRNA sequence...
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Species tree estimation from gene trees can be complicated by gene duplication and loss, and “gene tree parsimony” (GTP) is one approach for estimating species trees from multiple gene trees. In its standard formulation, the objective is to find a species tree that minimizes the total number of gene duplications and losses with respect to the input set of gene trees. Although much is known abou...
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We present a polynomial-time algorithm for finding an optimal set of taxa that maximizes the weighted-sum of the phylogenetic diversity across two phylogenetic trees. This resolves one of the challenges proposed as part of the Phylogenetics Programme held at the Isaac Newton Institute for Mathematical Sciences (Cambridge, 2007). It also completely closes the gap between optimizing phylogenetic ...
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ژورنال
عنوان ژورنال: Microbiome
سال: 2016
ISSN: 2049-2618
DOI: 10.1186/s40168-016-0153-6