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Search and Analysis
> ClustalW
ClustalW
Sequences
Protein
DNA
sequences
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Pairwise Alignment Parameters
Alignment Type:
Slow
Fast
Slow Pairwise Alignment Options
Protein Weight Matrix
BLOSUM
PAM
Gonnet
ID
DNA Weight Matrix
IUB
ClustalW
GAP OPEN
100
50
25
10
5
2
1
GAP EXTENSION
0.05
0.1
0.5
1.0
2.5
5.0
7.5
10.0
Fast Pairwise Alignment Options
KTUP (WORD SIZE)
1
2
3
4
5
WINDOW LENGTH
10
9
8
7
6
5
4
3
2
1
0
SCORE TYPE
percent
absolute
TOPDIAG
10
9
8
7
6
5
4
3
2
1
PAIRGAP
1
2
3
4
5
10
25
50
100
250
500
Multiple Sequence Alignment Parameters
Protein Weight Matrix
BLOSUM
PAM
Gonnet
ID
DNA Weight Matrix
IUB
ClustalW
GAP OPEN
100
50
25
10
5
2
1
GAP EXTENSION
0.05
0.20
0.5
1.0
2.5
5.0
7.5
10.0
GAP DISTANCES
10
9
8
7
6
5
4
3
2
1
NO END GAPS
no
yes
ITERATION
none
tree
alignment
NUMITER
1
2
3
4
5
6
7
8
9
10
CLUSTERING
NJ
UPGMA
OUTPUT Options
FORMAT
Aln w/numbers
Aln wo/numbers
GCG MSF
PHYLIP
NEXUS
NBRF/PIR
GDE
Pearson/FASTA
ORDER
aligned
input
