RAP / RapGreen r57
RAP is an algorithm and a software have been developed, which permit 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
RAP-Green is a new implementation and an improvment of the RAP software which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.
- Linux / Mac OsX / Windows
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Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G.
Bioinformatics. 2005 Jun 1;21(11):2596-603.