LOFT (Levels of Orthology From Trees) 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.
the Centre for Molecular and Biomolecular Informatics,the CMBI.
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René TJM van der Heijden,
Orthology prediction at scalable resolution by phylogenetic tree analysis,
BMC Bioinformatics 2007, 8:83