For better experience, turn on JavaScript!



KMAD is a software package specifically designed to construct multiple sequence alignments (MSAs) of so-called intrinsically disordered proteins (IDPs). IDPs differ from globular proteins by lacking tertiary structure and by having lower sequence conservation. The Authors provide both stand-alone and web server versions.


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


  • Operation: Multiple sequence alignment
  • Input: FASTA; plain protein sequences
  • Output: -
  • Software interface: Command-line user interface; web user interface
  • Language: C++
  • Operating system: Linux; Mac OS X
  • License: Free Software Foundation
  • Cost: Free
  • Version name: 1.15
  • Maturity: Stable
  • Credit: -
  • Contact: vriend _at_ | j.lange _at_
  • Collection: -


Lange J, Wyrwicz LS, Vriend G "KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins." Bioinformatics. 2016 Mar 15;32(6):932-6.
PMID: 26568635

Download and documentation

If you find errors, please report here.