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BLAST
ClustalW
HMMER
ClustalW @ VectorBase.org: New Multiple Alignment »
Directions:
Paste or upload sequences.
Select protein or dna sequences.
Optional:
Set additional ClustalW parameters.
Submit your ClustalW job.
Sequence Type:
Sequence Type:
protein
dna
ClustalW Options:
Parameters:
Default
[More options]
Alignment:
full
fast
kTuple (Word Size):
default
1
2
3
4
5
Window Length:
default
10
9
8
7
6
5
4
3
2
1
0
Score Type:
percent
absolute
Top Diagonals:
default
10
9
8
7
6
5
4
3
2
1
Gap Penalty:
default
1
2
3
4
5
10
25
50
100
250
500
Matrix:
GONNET (protein)
BLOSUM (protein)
PAM (protein)
Identity (both)
IUB (dna)
Open Gap Penalty:
default
1
2
5
10
25
50
100
End Gap Penalty:
default
10
20
Gap Extension Penalty:
default
0.05
0.5
1.0
2.5
5.0
7.5
10.0
Gap Separation Penalty:
default
10
9
8
7
6
5
4
3
2
1
Output Format:
aln
gcg MSF
phylip
pir
gde
nexus
Output Order:
aligned
input
Input Sequences (100Kb / 100 Sequence Limit):
Upload a file:
OR
Paste in sequences in FASTA format:
Job Control:
VectorBase Last Updated August 05th, 2008
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