CLUSTALW
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
actions_ - Excl - Actions
phylip_alig_ - Switch - Phylip alignment output format (-output)
Section: ****************************************************************************
multalign
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quicktree_ - Excl - Toggle Slow/Fast pairwise alignments (-quicktree)
typeseq_ - Excl - Protein or DNA (-type)
matrix_ - Excl - Protein weight matrix (-matrix)
dnamatrix_ - Excl - DNA weight matrix (-dnamatrix)
gapopen_ - Integer - Gap opening penalty (-gapopen)
gapext_ - Float - Gap extension penalty (-gapext)
endgaps_ - Switch - End gap separation penalty (-endgaps)
gapdist_ - Integer - Gap separation pen. range (-gapdist)
pgap_ - Switch - Residue specific penalties (Pascarella gaps) (-nopgap)
hgap_ - Switch - Hydrophilic gaps (-nohgap)
hgapresidues_ - List - Hydrophilic residues list (-hgapresidues)
maxdiv_ - Integer - Delay divergent sequences : % ident. for delay (-maxdiv)
negative_ - Switch - Negative values in matrix ? (-negative)
transweight_ - Float - Transitions weight (between 0 and 1) (-transweight)
usetree_ - InFile - File for old guide tree (-usetree)
Section: ****************************************************************************
fastpw
*************************************************************************************
ktuple_ - Integer - Word size (-ktuple)
topdiags_ - Integer - Number of best diagonals (-topdiags)
window_ - Integer - Window around best diags (-window)
pairgap_ - Float - Gap penalty (-pairgap)
score_ - Excl - Percent or absolute score ? (-score)
Section: ****************************************************************************
slowpw
*************************************************************************************
pwmatrix_ - Excl - Protein weight matrix (-pwmatrix)
pwdnamatrix_ - Excl - DNA weight matrix (-pwdnamatrix)
pwgapopen_ - Float - Gap opening penalty (-pwgapopen)
pwgapext_ - Float - Gap extension penalty (-pwgapext)
Section: ****************************************************************************
trees
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kimura_ - Switch - Use Kimura's correction (multiple substitutions) ? (-kimura)
tossgaps_ - Switch - Ignore positions with gaps ? (-tossgaps)
bootstrap_ - Integer - Bootstrap a NJ tree (give the number of bootstraps, 0 for none) (-bootstrap)
bootlabels_ - Excl - Phylip bootstrap positions (-bootlabels)
seed_ - Integer - Seed number for bootstraps (-seed)
outputtree_ - Excl - Output tree/distance format (-outputtree)
Section: ****************************************************************************
outputparam
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output_ - Excl - Output format (-output)
gde_lower_ - Switch - Upper case GDE output (-case)
outorder_ - Excl - Result order (-outorder)
seqnos_ - Switch - Output sequence numbers in the output file (clustalw format) (-seqnos)
aligfile_ - Results -
readseq_ok_aligfile_ - Results -
newtreefile_ - Results -
phylipnewtreefile_ - Results -
Section: ****************************************************************************
profile
*************************************************************************************
profile1_ - InFile - Profile 1 (-profile1)
profile2_ - InFile - Profile 2 (-profile2)
usetree1_ - InFile - File for old guide tree for profile1 (-usetree1)
usetree2_ - InFile - File for old guide tree for profile2 (-usetree2)
newtree1_ - OutFile - File for new guide tree for profile1 (-newtree1)
newtree2_ - OutFile - File for new guide tree for profile2 (-newtree2)
Section: ****************************************************************************
structure
*************************************************************************************
nosecstr1_ - Switch - Use profile 1 secondary structure / penalty mask (-nosecstr1)
nosecstr2_ - Switch - Use profile 2 secondary structure / penalty mask (-nosecstr2)
helixgap_ - Integer - Helix gap penalty (-helixgap)
strandgap_ - Integer - Strand gap penalty (-strandgap)
loopgap_ - Integer - Loop gap penalty (-loopgap)
terminalgap_ - Integer - Secondary structure terminal penalty (-terminalgap)
helixendin_ - Integer - Helix terminal positions: number of residues inside helix to be treated as terminal (-helixendin)
helixendout_ - Integer - Helix terminal positions: number of residues outside helix to be treated as terminal (-helixendout)
strandendin_ - Integer - Strand terminal positions: number of residues inside strand to be treated as terminal (-strandendin)
strandendout_ - Integer - Strand terminal positions: number of residues outside strand to be treated as terminal (-strandendout)
secstrout_ - Excl - Output in alignment (-secstrout)