It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events. With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research. more detailed and accurate orthology information since it can effectively distinguish main orthologs from inparalogs. 1. INTRODUCTION According to the definition of Fitch 10, orthologs are genes that evolved by speciation, while paralogs are genes that evolved by duplication. Orthologs typ-ically occupy the same functional niche in different AbstractOrthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A Read More. Full Text HTML; Download PDF Therefore, out-paralogs might erroneously be inferred as orthologs when true orthologs are physically absent. Given the two real examples of gene losses in Figure 3 , it is demonstrated that, unlike tree-reconciliation, a graph-based approach cannot distinguish between orthologs and out-paralogs in the presence of multiple gene loss evens ( Figure 3 a). owering plant genomics, an evolutionary domain characterized by recurrent wgd events. The massive data set we analyze is described in Section 3. In addition there is a weight represent the representing a protein similarity score. Let decomposition of Fig.1. Homology set, showing erroneous" edges between orthology sets. The usefulness of orthologs and paralolgs in modern genomics comes from the fact that orthologs generally perform the same function while paralogs perform similar functions. The reconstruction of orthologs and paralogs at each node of the evolution-ary tree can shed light on the evolution of function. We can give several examples how the knowledge of It relies on the species overlap algorithm (Huerta-Cepas et al. 2007, 2016) to identify pairs of orthologous genes in a phylogeny, and processes this output to identify groups of orthologs (defined as homologs descending from a single gene at the user-defined taxonomic scope), propagate gene name annotations, and report evolutionary relationships between gene pairs. Orthologs have primarily been used as evolutionary markers for inferring species phylogenies because they follow species divergence 17, 18, but they can be used to link functionally equivalent genes across genomes and, as such, enable the function of an unknown protein to be inferred using known (i.e. functionally characterized) orthologs in other species 5, 19. To ensure continuity of the updated pVOGs database with the previous dataset of virus orthologs and measure the differences resulting from splitting proteins into domains vs. using full-length proteins, the clustering of viral proteins into orthologous groups in the 'pVOGs 2016' dataset was compared to that in the older 'POGs 2013' dataset (Table (Table1) 1) for a reduced dataset The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplica- (ed.), Evolutionary Genomics: Statistical and Computational Methods, Methods in Molecular Biology, vol. 1910, http