PipMaker is a web-based tool designed for comparing two long genomic DNA sequences to identify conserved segments and produce high-resolution displays of alignments. The primary output, a percent identity plot (pip), shows the position and similarity of each aligning segment between the two sequences in a compact and understandable format. The web site also provides a dot plot showing the locations of aligning segments in both species. PipMaker is suitable for comparing sequences from any related species, with the ability to handle unfinished or "working draft" sequences. It uses the BlastZ alignment program and can handle sequences up to 2 million base pairs in length. The tool is useful for identifying protein-coding regions, regulatory elements, and patterns of sequence changes during evolution. Examples are provided for mammalian, nematode, and bacterial sequences, demonstrating its effectiveness in various contexts. Advanced features include the ability to choose scoring matrices, remove duplicate alignments, and handle single coverage scenarios.PipMaker is a web-based tool designed for comparing two long genomic DNA sequences to identify conserved segments and produce high-resolution displays of alignments. The primary output, a percent identity plot (pip), shows the position and similarity of each aligning segment between the two sequences in a compact and understandable format. The web site also provides a dot plot showing the locations of aligning segments in both species. PipMaker is suitable for comparing sequences from any related species, with the ability to handle unfinished or "working draft" sequences. It uses the BlastZ alignment program and can handle sequences up to 2 million base pairs in length. The tool is useful for identifying protein-coding regions, regulatory elements, and patterns of sequence changes during evolution. Examples are provided for mammalian, nematode, and bacterial sequences, demonstrating its effectiveness in various contexts. Advanced features include the ability to choose scoring matrices, remove duplicate alignments, and handle single coverage scenarios.