Gene-warp is a tool to select ortholog pairs with best alignments and to explore alignment paths (not expression profiles!) shared by many genes. The program takes as an input two related datasets, containing profiles of orthologous genes.
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Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.