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For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations <jats:italic>between<\/jats:italic> the orthologous groups.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We introduce \"<jats:italic>levels of orthology<\/jats:italic>\" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The \"<jats:italic>levels of orthology<\/jats:italic>\" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.cmbi.ru.nl\/LOFT\" ext-link-type=\"uri\">http:\/\/www.cmbi.ru.nl\/LOFT<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-8-83","type":"journal-article","created":{"date-parts":[[2007,3,8]],"date-time":"2007-03-08T19:02:15Z","timestamp":1173380535000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":109,"title":["Orthology prediction at scalable resolution by phylogenetic tree analysis"],"prefix":"10.1186","volume":"8","author":[{"given":"Ren\u00e9 TJM","family":"van der Heijden","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Berend","family":"Snel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vera","family":"van Noort","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martijn A","family":"Huynen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,3,8]]},"reference":[{"issue":"4","key":"1455_CR1","doi-asserted-by":"publisher","first-page":"COMMENT1005","DOI":"10.1186\/gb-2001-2-4-comment1005","volume":"2","author":"EV Koonin","year":"2001","unstructured":"Koonin EV: An apology for orthologs - or brave new memes. 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