Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences



  1. What is PROBCONS?
  2. How do I cite PROBCONS?
  3. How do I align sequences using PROBCONS?


PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date.


How do I cite PROBCONS?

Publications using the PROBCONS tool should cite:


How do I align sequences using PROBCONS?

To align sequences, you may

  1. Use the command-line interface for PROBCONS. This requires you to download and install the PROBCONS program on your local machine; the source code for the program is available here. A description of the command-line arguments that can be used with the program are given in the manual for the program, also available on the download page.
  2. Use the web interface for PROBCONS. PROBCONS provides a web server for aligning protein sequences. To use the web server, which is located here, first specify the e-mail address to which all results will be sent. Then, browse and attach the MFA format input sequences to be aligned. Finally, choose the desired additional option settings, though the defaults should work fine for most people. Note that PROBCONS is able to generate output in both MFA and CLUSTALW output formats.