PROBALIGN
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
alignment_order_ - Switch - Print sequences in alignment order rather than input order (-a)
scoring_matrix_ - Excl - Sequence Type (Protein specifies gonnet 160; Nucleic acid specifies simple)
output_format_ - Switch - ClustalW output format (-clustalw)?
Section: ****************************************************************************
dna_params
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gapopenn_ - Float - Gap Open Penalty (-go, recommended = 4.0)
gapextn_ - Float - Gap Extension Penalty (-ge, recommended = 0.25)
temp_na_ - Float - Temperature for Nucleic Acid (-T, recommended = 1.0)
Section: ****************************************************************************
prot_params
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gapopenp_ - Float - Protein Gap Open Penalty (-go, recommended = 22)
gapextp_ - Float - Gap Extension Penalty (-ge, recommended = 1)
temp_aa_ - Float - Temperature for Amino Acids (-T, recommended = 5)
output_files_ - Results -