Phyrex (PHYlogenetic REconstruction by use of gene eXpression and alternate mRNA splicing patterns) is a program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences.
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BMC Bioinformatics. 2005 May 27;6:127.
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
Rossnes R, Eidhammer I, Liberles DA.