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RESOURCES
Databases with MKT estimates
DPDB
MamPol
Sequence Analysis Tools
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NAME OF THE ANALYSIS:
TYPES OF SITES TO ANALYZE:
(Only comparisons involving two mutually exclusive types of site are allowed)
SET AS NEUTRAL
(The Neutral Class selected will be compared to another type of site)
Analyze synonymous changes
Analyze non-synonymous changes
Analyze four-fold degenerate sites/changes
?
Analyze two-fold degenerate sites/changes
?
Analyze non-degenerate sites/changes
?
PASTE THE SEQUENCES
(
)
(Format must be FASTA)
Species 1
Upload a file
:
Species 2
Upload a file
:
ANNOTATIONS
Species 1
Species 2
* If you uploaded a file with the sequences, please write a line foreach sequence with its annotations as follows:
Sequence 1 --> 1..500
from the first position until the position 500
Sequence 2 --> 1..200,205..500
from the first position until the position 200, and from the position 250 until the position 500
etc.
EXCLUDE LOW FREQUENCY VARIANTS
≤
%
CHOOSE THE GENETIC CODE:
Universal Code
Vertebrate Mitochondrial Code
Yeast Mitochondrial Code
Mold, Protozoan and Coelenterate Mit. Code and Mycoplasma/Spiroplasma Code
Invertebrate Mitochondrial Code
Ciliate, Dasycladacean and Hexamita Nuclear Code
Echinoderm and Flatworm Mitochondrial Code
Euplotid Nuclear Code
Bacterial and Plant Plastid Code
Alternative Yeast Nuclear Code
Ascidian Mitochondrial Code
Alternative Flatworm Mitochondrial Code
Blepharisma Nuclear Code
Chlorophycean Mitochondrial Code
Trematode Mitochondrial Code
Scenedesmus obliquus Mitochondrial Code
Thraustochytrium Mitochondrial Code
ALIGN SEQUENCES
ALIGNMENT ORDER:
Species independently, then join
All sequences at the same time
CHOOSE THE ALIGNMENT PROGRAM:
MUSCLE
CLUSTALW2.0
SET THE ALIGNMENT PARAMETERS:
Output Format:
ClustalW
FASTA
HTML
Phylip sequential
Create a Log file
Output Tree
None
From first iteration
From second iteration
Penalties:
Gapopen
Gapextend
Center
Diagonals:
Maximum Trees
Maximum Iterations
0
-1
-2
-4
-6
-8
-10
-12
-14
-16
-18
-20
0.0
-0.1
-0.2
-0.3
-0.4
-0.5
-0.6
-0.8
-1.0
-1.2
-1.4
-1.6
-1.8
-2.0
0.0
Unabled
Diagonals
Diagonals 1
Diagonals 2
1
2
3
4
5
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
SET THE ALIGNMENT PARAMETERS:
FAST PAIRWISE ALIGNMENT
Ktup
Window Length
Score type
Top Diagonals
Pairgap
1
2
3
4
5
10
9
8
7
6
5
4
3
2
1
0
percent
absolute
10
9
8
7
6
5
4
3
2
1
1
2
3
4
5
10
25
100
250
500
MULTIPLE ALIGNMENT
Gap Open
No End Gaps
Gap Extension
Gap Distances
100
50
25
10
5
2
1
yes
no
0.05
0.5
1.0
2.5
5.0
7.5
10.0
10
9
8
7
6
5
4
3
2
1
Transition weight
Delay divergent sequences (%)
Iteration
Number Iterations
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
10
20
30
40
50
60
70
80
90
None
Tree
Alignment
1
2
3
4
5
6
7
8
9
10
OUTPUT FORMAT
Clustal w/num
Clustal wo/num
GCG
GDE
Phylip
PIR
Nexus
