Pipviewer is a visualizer for multiple alignments of genomic sequences. Pipviewer highlights conserved regions and allows basic annotations. Its main goal is to find conserved probes for the construction of gene order data sets.
Selected regions marked as 'probes' can be exported to faster format. It can also retrieve gene annotations form the NBCI and display this information along the alignment. Pipviewer is not an aligner. You must compute the alignment with another tool like Clustal or Multi PIP Maker.