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probalign website  

Probalign uses partition function posterior probability estimates to compute maximum expected accuracy multiple sequence alignments. It performs statistically significantly better than the leading alignment programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on datasets containing N/C terminal extensions and on datasets with long and heterogeneous length sequences. On heteregeneous length datasets containing repeats Probalign alignment accuracy is 10% and 15% than the other three methods when standard deviation of length is at least 300 and 400.

Required Modules


  • probalign

System Variables

  • HPC_{{#uppercase:probalign}}_DIR - installation directory


If you publish research that uses probalign you have to cite it as follows:

S. Chikkagoudar, U. Roshan and D. R. Livesay, eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities, Nucleic Acids Research, Vol 35, 2007, W675-W677 [1].


  • Validated 4/5/2018