RAP-Green
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RAP is a tree reconciliation software, which permits to find gene duplications in phylogenetic trees, in order to improve gene function inferences. The algorithm is applicable to realistic data, especially n-ary species tree and unrooted phylogenetic tree. The algorithm also takes branch lengths into account. RAP-Green is a revamped version, adapted to plants, and able to provide confidence scores for orthology relationships, from a functional point of vue. (Dufayard 2011)