multiple sequence alignment software

PAGAN is a general-purpose method for the alignment of sequence graphs. It includes e.g.:

  • phylogenetic multiple sequence alignment
  • alignment extension by phylogenetic sequence placement
  • modelling of Roche 454 sequencing error
  • alignment and placement of NGS sequences
  • pileup alignment of similar/noisy NGS reads or sequences
  • inference of ancestral sequences


PAGAN documentation is available at the Wiki page. PAGAN source code is available with git.

PAGAN is under development. If you have questions, comments or suggestions how to improve the method, please post them through thePAGAN discussion group. Bug reports can be entered through the Issues page.

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