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Stratigraphically constrained cluster analysis is a multivariate method for quantitative definition of stratigraphic zones. As opposed to ordinary, unconstrained cluster analysis, only stratigraphically adjacent clusters are considered for merging. The method of incremental sum of squares has been used widely for unconstrained analyses and has proved particularly satisfactory for pollen frequency data. CONISS is a FORTRAN 77 program for stratigraphically constrained cluster analysis by this method. Several data transformations lead to different implicit dissimilarity coefficients. As an option, the program also will perform an unconstrained analysis, which can be useful for comparison with the constrained analysis.