DCA
1.1
Divide-and-Conquer Multiple Sequence Alignment
J. Stoye
A.W.M. Dress, G. Füllen, S.W. Perrey, A Divide and Conquer Approach to Multiple Alignment, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB 95), AAAI Press, Menlo Park, CA, USA, 107-113, 1995.
J. Stoye, Multiple Sequence Alignment with the Divide-and-Conquer Method, Gene 211(2), GC45-GC56, 1998. (Gene-COMBIS)
alignment:multiple
dca
dca
perl
"dca"
0
seq
Sequences File
perl
" $value"
8
100
seqsfile
perl
1
outfile
dca.out
readseq_ok_alig
perl
$suppress_output && ($output_format eq "2" || $output_format eq "3")
control
Control parameters
cost
Cost matrix (default: depends on sequences) (-c)
perl
($value)? " -c $value" : ""
1
blosum30
blosum45
blosum62
pam160
pam250
unitcost
dna
rna
dnarna
gaps
Penalize end gaps as internal gaps (default: free shift) (-g)
perl
($value)? " -g":""
0
1
approximate
Use approximate cut positions (-a)
perl
($value)? " -a":""
1
1
On: FastDCA (use approximate cut positions); Off: slower, more accurate algorithm (search for eaxct cut positions)
intensity
Weight intensity (-b)
perl
(defined $value && $value != $vdef)? " -b $value" : ""
0.0
1
Weight intensity must be >= 0.0 and <= 1.0
perl
$intensity < 0.0 || $intensity > 1.0
recursion
Recursion stop size (-l)
perl
($value && $value != $vdef)? " -l $value" : ""
30
1
5 ... 100 recommended; small: faster algorithm, maybe worse.
window
Window size (-w)
perl
($value != $vdef)? " -w $value" : ""
0
1
To correct the alignment in the proximity of division sites, the sequences can be re-aligned inside a window of size w >= 0 placed across each slicing site.
output
Output parameters
quiet
perl
" -q"
1
output_format
Output format (-f)
perl
($value && $value ne $vdef)? " -f $value" : ""
2
1
1
2
3
4
suppress_output
Suppress output about progress of the program (-o)
perl
($value)? " -o":""
1
1