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We have developed Domainoid, a new tool aiming to overcome these challenges faced by full-length orthology methods by inferring orthology on the domain level. ... This domain-oriented approach allows detection of discordant domain orthologs, cases where different domains on the same protein have different evolutionary histories. ... We further thank the Quest for Orthologs consortium for valuable discussions highlighting the need for domain-wise orthology inference. ...doi:10.1186/s12859-019-3137-2 pmid:31660857 pmcid:PMC6816169 fatcat:v4ktvdshebcczb7jxb24g6vtai