SeqAn::T-Coffee is an open source multiple sequence alignment program. SeqAn::T-Coffee aligns aminoacid, DNA and RNA sequences using a consistency-based progressive alignment algorithm on a graph of sequence segments.


Please Cite

  • T. Rausch, A.-K. Emde, D. Weese, C. Notredame, K. Reinert, “Segment-based multiple sequence alignment”, vol. 24, iss. 16, 2008.
    cite this publication
     abstract = {Motivation: Many multiple sequence alignment tools have been developed      in the past, progressing either in speed or alignment accuracy. Given
    the importance and wide-spread use of alignment tools, progress in
    both categories is a contribution to the community and has driven
    research in the field so far. Results: We introduce a graph-based
    extension to the consistency-based, progressive alignment strategy.
    We apply the consistency notion to segments instead of single characters.
    The main problem we solve in this context is to define segments of
    the sequences in such a way that a graph-based alignment is possible.
    We implemented the algorithm using the SeqAn library and report results
    on amino acid and DNA sequences. The benefit of our approach is threefold:
    (1) sequences with conserved blocks can be rapidly aligned, (2) the
    implementation is conceptually easy, generic and fast and (3) the
    consistency idea can be extended to align multiple genomic sequences.
    Availability: The segment-based multiple sequence alignment tool
    can be downloaded from A novel
    version of T-Coffee interfaced with the tool is available from
    The usage of the tool is described in both documentations. Contact:},
     author = {T. Rausch and A.-K. Emde and D. Weese and C. Notredame and K. Reinert},
     journal = {Bioinformatics},
     number = {16},
     pages = {i187--192},
     title = {Segment-based multiple sequence alignment},
     url = {},
     volume = {24},
     year = {2008}


For questions, comments, or suggestions please contact:

Tobias Rausch