Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
نویسندگان
چکیده
منابع مشابه
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Motivation Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is nec...
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Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest. Identifying such groups is useful in a wide range of contexts, including inference of gene function, study of gene evolution dynamics and comparative genomics. Hierarchical orthologous groups can be derived from reconciled gene/species trees but, t...
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Figure 1 shows a toy example to illustrate the analysis. The observed itens in Figure 1a are distributed evenly among the different species (i.e. high diversity), while Figure 1b shows the opposite case. The diversity is given by the normalized Shannon’s diversity and represents the distribution of orthologous and paralogous genes in a set of species. High diversity represents an homogeneous di...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2017
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btx229