MULTICOMP is a program that assists in the phylogenetic analysis of DNA sequences. It streamlines sequence handling and analysis. Input is from either individual sequence files or a file of aligned sequences. It produces data on variation at DNA and amino acid sequence level and can also convert sequences to data formats suitable for PHYLIP, PAUP and MacClade phylogenetic inference programs. Further, two tree-building programs, NEIGHBOR and DNAPARS, of PHYLIP can be directly run from within it. MULTICOMP performs Sawyer's algorithm for detection of gene conversion. The program facilitates analysis using only part of the data of a data set or using two or more combined data sets.