Accurate Multiple Alignment: ProbCons

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ProbCons Homepage
Using the MPI Bioinformatics Toolkit for ProbCons and other multiple alignment packages: Go to the website: http://toolkit.tuebingen.mpg.de and familiarize yourself with the different options. Send email to: mpi-toolkit@tuebingen.mpg.de with subject header: Registration , (and with no email content). The website manager will send you a username and password. Log in and use (the service is free). See also the following paper: Biegert, A. et al. 2006. "The MPI Bioinformatics Toolkit for protein sequence analysis." Nucleic Acids Research, 34, Web Server Issue, W335-W339.
Foundation paper:

Do, C.B., M.S.P. Mahabhashyam, M. Brudno, and S. Batzoglou. 2005. ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research, 15: 330-340.

Comparison Paper: Edgar, R.C. and S. Batzoglou. 2006. "Multiple Sequence Alignment," Current Opinions in Structural Biology, 16 : 368-373. (This paper compares CLUSTALW, MUSCLE, T-COFFEE, ProbCons, DIALIGN, MAFFT, and ProDA.)