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. 2020 Sep 4;38(2):727–734. doi: 10.1093/molbev/msaa224

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© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 1. — Impact of paralogs and xenologs on the inference of gene orthology. Scenario (A): No paralogs/xenologs. The orthologous gene is present in all the genomes; no paralogs or xenologs are present. Scenario (B): Within-paralogs/xenologs. The orthologous gene is present in all the genomes; one or more within-paralog/xenolog sequences are present. Scenario (C): Partially hidden paralogs/xenologs. The orthologous gene is missing in some genomes; some genomes are missing the orthologous sequence but contain a paralogous or a xenologous sequence (hidden paralog/xenolog); other genomes contain both the orthologous sequence and the paralogous or xenologous sequence (within-paralog/xenolog). Scenario (D): Completely hidden paralogs/xenologs. Some genomes are missing the orthologous sequence but contain a paralogous or a xenologous sequence (hidden paralog/xenolog); no within-paralogs/xenologs are present in other genomes. Plain boxes represent orthologous sequences; striped boxes represent paralogous or xenologous sequences. Scenarios A and B are expected to yield straightforward core gene predictions by BBH-based methods and CoreCruncher. Scenarios C and D will likely lead to the inclusion of paralogous and xenologous sequences in the core genome constructed with BBH-based approaches.