Nucleotideand aminoacidsequences research is actual for molecular biology and bioengineering. An important aspect of analysis of such sequences is multiple alignment. This article discusses the implementations of the MUSCLE and ClustalW programs on multiprocessors and a web interface to them. The modification of the MUSCLE algorithm realize a data-flow manner of sequence alignment. It uses the PARUS system to build a data-flow graph and execute this graph on one multiprocessor as a MPI-program. The data-flow algorithm has been tested on the sequences of human Long Terminal Repeats class five (LTR5) and several other examples.