AL2CO - calculation of position conservation for a multiple sequence alignment

Options:


sequence weighting scheme:
        Sequence weighting corrects for biased representation of similar sequences in an alignment.
        Options:
        0=unweighted,
        1=weighted by the modified method of Henikoff & Henikoff,
        2=independent-count based
        Default = 2
        
conservation calculation method:
        Options:
        0=entropy-based    C(i)=sum_{a=1}^{20}f_a(i)*ln[f_a(i)], where f_a(i)
          is the frequency of amino acid a at position i,
        1=variance-based   C(i)=sqrt[sum_{a=1}^{20}(f_a(i)-f_a)^2], where f_a
          is the overall frequency of amino acid a,
        2=sum-of-pairs measure   C(i)=sum_{a=1}^{20}sum_{b=1}^{20}f_a(i)*f_b(i)*S_{ab},
          where S_{ab} is the element of a scoring matrix for amino acids a and b
        Default = 0

scoring matrix  
        This is only for the conservation calculation method of sum-of-pairs measure.
        Options:
        0=BLOSUM62 matrix
        1=identity matrix
        Default = 0

scoring matrix transformation  
        This is only for the conservation calculation method of sum-of-pairs measure.
        Options:
        0=no transformation,
        1=normalization S'(a,b)=S(a,b)/sqrt[S(a,a)*S(b,b)],
        2=adjustment S"(a,b)=2*S(a,b)-(S(a,a)+S(b,b))/2
        Default = 0
        
window size used for averaging conservation (for smoothing purpose): 
        Default = 1
        Recommended value for motif analysis: 3

normalize conservation values:
        Subtract the mean from each conservation index and divide by the
        standard deviation.
        Default = True

exclude the first sequence from calculation:   
        If set to true, the first sequence in the alignment will not
        be included in the conservation calculation.
        Default = False
        
gap fraction above which conservation calculation is not performed:         
        The value should be more than 0 and no more than 1. Conservation
        indices are calculated only for positions with gap fraction less
        than the specified value. Otherwise, conservation indices will
        be set to M-S, where M is the mean conservation value and S is
        the standard deviation.
        Default = 0.5

Block size of the output alignment file with conservation indices: 
        The number of residues in a line of each block in output alignment 
        with conservation indices.
        Default = 70


pdb file for which b-factor field is replaced with conservation (optional):          
        The sequence in the pdb file should match exactly the first sequence of
        the alignment. Results include a link to a pdb file with b-factor field
        replaced by conservation values so that conservation information can be 
        mapped onto a structure and displayed.