For better experience, turn on JavaScript!



DIALIGN 2 is an improved version of the original multiple sequence alignment tool DIALIGN from the year 1997. This tool uses sequence segments that don't contain indels for alignment construction. The most recent version of DIAGLIGN is called DIALIGN-TX. See the 'LINKS'.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Multiple alignment; Alignment; Sequence alignment; Multiple sequence alignment
  • Input: FASTA
  • Output: DIALIGN; FASTA
  • Software interface: Command-line user interface; Web user interface
  • Language: C
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU Lesser General Public License version 2.1
  • Cost: Free
  • Version name: 2.2.1
  • Maturity: Mature
  • Credit: -
  • Contact: bmorgen _at_
  • Collection: DIALIGN


Morgenstern B "DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment." Bioinformatics. 1999 Mar;15(3):211-8.
PMID: 10222408

Morgenstern B, Dress A, Werner T "Multiple DNA and protein sequence alignment based on segment-to-segment comparison." Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12098-103.
PMID: 8901539

Morgenstern B, Frech K, Dress A, Werner T "DIALIGN: finding local similarities by multiple sequence alignment." Bioinformatics. 1998;14(3):290-4.
PMID: 9614273

Download and documentation

If you find errors, please report here.