Phylogeny reconstruction using duplicate genes

in this paper, we propose a new method (uninode coding) for coding duplicat e (paralogous) genes to infer species trees. Uninode coding incorporates da ta from duplicated and unduplicated gene copies in phylogenetic analyses of taxa. Uninode coding utilizes global parsimony through the inclusion of bo th duplicated and unduplicated gene copies, allows one to code all data sou rces from a taxon into a single terminal, and overcomes problems of charact er dependence among duplicated and unduplicated gene copies. We present an example of uninode coding using the phytochrome A and phytochrome C data fr om a study by Donoghue and Mathews.