M-align is to align (non-linear resampling) the input data sets based on alignment matrices (*.ali files, see also Figure 7F) produced by Time-warp or Gene-warp programs. The alignment matrices can also be adjusted/generated manually with the account of E-maps. M-align takes as an input two matrices used to generate alignment matrix (*.ali) or two matrices with equivalent number of columns (time points) plus the alignment matrix (*.ali) itself.
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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.