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MSACompro is a tool to integrate tool predicted secondary structure, residue contact information, and relative solvent accessibility into a posterior probability for multiple sequence alignment (MSA) software, such as MSAProbs, ProbCons, Probalign, T-coffee, MAFFT, and MUSCLE.


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


  • Operation: Multiple sequence alignment; protein structure prediction
  • Software interface: Command-line user interface
  • Language: Perl;C++
  • Operating system: Linux
  • License: Other
  • Cost: Free for non-commercial usage.
  • Version name: 1.2.0
  • Maturity: Stable
  • Credit: NIH R01 grant (no. 1R01GM093123)
  • Contact: Jianlin Cheng chengji _at_
  • Collection: -


Deng X, Cheng J "MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts." BMC Bioinformatics. 2011 Dec 14;12:472.
PMID: 22168237

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