Time-warp is the global alignment program; several alternative methods are available to generate a similarity matrix; a dynamic programming algorithm finds the optimal alignment path through the matrix. As well as the Gene-warp (see above), Time-warp takes as an input two time-series microarray datasets, containing orthologous expression profiles in the corresponding rows of the two matrices.
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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.