Chromaligner is a tool for chromatogram alignment. It could be used for chromatograms generated by various chromatographic methods such as high performance liquid chromatography and capillary electrophoresis. Time shift is a frequent encountered problem in gradient elution or capillary electrophoresis. Chromaligner used a constrained chromatogram alignment method to resolve this issue.

Chromaligner aligns chromatograms based on correlation optimized warping with optional alignment on predefined peaks. The inputs of Chromaligner include a set of chromatograms comprising intensity, retention time and constraints if there are any. The constraints are the common user-defined peaks (or predefined peaks) or automatically assigned by Chromaligner by mapping the full chromatogram. The outputs files from Chromaligner are aligned chromatograms along with overlaid chromatogram before and after alignment.