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Start Your TrialProbalign 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 heterogeneous 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.
toolId=PROBALIGN
Supported parameters:
input.infile_ - Primary Input File
vparam.runtime_ - Float - Maximum Hours to Run default=1.0, max = 72
vparam.alignment_order_ - Switch - Print sequences in alignment order rather than input order (-a) (default=0)
vparam.scoring_matrix_ - Excl - Sequence Type (gonnet 160 (for protein) nuc_simple (for DNA) default= nuc_simple
vparam.output_format_ - Switch - ClustalW output format (-clustalw)? (default=0)
vparam.gapopenn_ - Float - Gap Open Penalty (-go, recommended = 4.0)
vparam.gapextn_ - Float - Gap Extension Penalty (-ge, recommended = 0.25)
vparam.temp_na_ - Float - Temperature for Nucleic Acid (-T, recommended = 1.0)
vparam.gapopenp_ - Float - Protein Gap Open Penalty (-go, recommended = 22)
vparam.gapextp_ - Float - Gap Extension Penalty (-ge, recommended = 1)
vparam.temp_aa_ - Float - Temperature for Amino Acids (-T, recommended = 5)