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(1) Sequence comparison
(2) Nucleotide Diversity
Clustal
Jalview
SNPs-Graphic
PDA Server
ClustalW
(Ver. 1.83)
(Default parameters have been optimized for polymorphism analyses)
ClustalW Help
GENERAL SETTINGS
ALIGNMENT TITLE
ALIGNMENT
TYPE
OUTPUT
FORMAT
OUTPUT
ORDER
SLOW
FAST
automatic
protein
DNA
clustal w/num
clustal wo/num
gcg MSF
phylip
pir
gde
aligned
input
FAST PAIRWISE ALIGNMENT
KTUP
(WORD SIZE)
WINDOW LENGTH
SCORE TYPE
TOPDIAG
PAIRGAP
def: 1
2
3
4
5
10
9
8
7
6
def: 5
4
3
2
1
0
def: percent
absolute
10
9
8
7
6
def: 5
4
3
2
1
1
2
def: 3
4
5
10
25
50
100
250
500
MULTIPLE ALIGNMENT
MATRIX
GAP OPEN
END GAPS
GAP EXTENSION
GAP DISTANCES
BLOSUM
def: PAM
GONNET
ID
100
def: 50
25
10
5
2
1
def: 10
20
def: 0.05
0.5
1.0
2.5
5.0
7.5
10.0
10
9
8
7
6
5
4
3
def: 2
1
PHYLOGENETIC
TREE
*
(*Introduce an
alignment
in one of the accepted formats: NBRF/PIR, EMBL/SwissProt, Pearson/FASTA, GDE, Clustal, GCG/MSF, RSF)
TREE TYPE
CORRECT DIST.
IGNORE GAPS
def: none
nj
phylip
dist
def: off
on
def: off
on
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