MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences

Curr Protoc Bioinformatics. 2010 Jun;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s30.


The MultiPipMaker World Wide Web server ( provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide-level multiple alignment and/or stacked, pairwise percent identity plots, and support for user-specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented.

Publication types

  • Comparative Study

MeSH terms

  • Base Sequence
  • Computational Biology / methods*
  • Genome / genetics
  • Guidelines as Topic
  • Internet*
  • Sequence Alignment / methods*
  • Software*