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A web-based tool for multiple sequence alignment (MSA) of DNA. The algorithm uses PFAM or profiles provided by a user. The web interface requires registration and login.


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


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: -
  • Software interface: Web user interface
  • Language: -
  • Operating system: Linux; MAC OS X; Microsoft Windows
  • License: Not stated
  • Cost: Free
  • Version name: 2.0
  • Credit: The Italian nodes of Lifewatch and ELIXIR Research Infrastructure.
  • Contact:
  • Collection: -


Balech B, Monaco A, Perniola M, Santamaria M, Donvito G, Vicario S, Maggi G, Pesole G "DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method." Methods Mol Biol. 2018;1746:173-180.
PMID: 29492894

Balech B, Vicario S, Donvito G, Monaco A, Notarangelo P, Pesole G "SA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information." Bioinformatics. 2015 Aug 1;31(15):2571-3.
PMID: 25819080

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