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Multiple alignment ( Name: Vigan.02G001800.01 )
Species
Vigna angularis [1]
Vigna angularis (paralogs) [1]
Arabidopsis thaliana [1]
Glycine max [1]
Medicago trancatula [1]
Populus trichocarpa [1]
Phaseolus vulgaris [1]
Vigna radiata [1]
Multiple Ortholog Sequences
Use representative sequences
Use all sequences
Program
Clustalw
MAFFT
Option
Sequence Type
PROTEIN
CDS
transcript
Clustalw Option
General Setting Parameters
:
Output Format
:
CLUSTAL
GCG(MSF)
GDE
PIR
Phylip
FASTA
Pairwise Alignment:
FAST/APPROXIMATE
SLOW/ACCURATE
Pairwise Alignment Parameters
:
For FAST/APPROXIMATE
:
K-tuple(word) size:
Window size:
Gap Penalty:
Number of Top Diagonals:
Scoring Method:
PERCENT
ABSOLUTE
For SLOW/ACCURATE
:
Gap Open Penalty:
Gap Extension Penalty:
Select Weight Matrix:
BLOSUM (for PROTEIN)
PAM (for PROTEIN)
GONNET (for PROTEIN)
ID (for PROTEIN)
IUB (for DNA)
CLUSTALW (for DNA)
(Note that only parameters for the algorithm specified by the above "Pairwise Alignment" are valid.)
Multiple Alignment Parameters
:
Gap Open Penalty:
Gap Extension Penalty:
Weight Transition:
YES (Value:
)
NO
Hydrophilic Residues for Proteins:
Hydrophilic Gaps:
YES
NO
Select Weight Matrix:
BLOSUM (for PROTEIN)
PAM (for PROTEIN)
GONNET (for PROTEIN)
ID (for PROTEIN)
IUB (for DNA)
CLUSTALW (for DNA)
MAFFT Option
Strategy
:
Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size.
L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information)
G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information)
E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences)
FFT-NS-i (iterative refinement method; max. 1000 iterations)
FFT-NS-2 (fast; progressive method)
FFT-NS-1 (very fast; recommended for <2000 sequences; progressive method with a rough guide tree)
NW-NS-i (iterative refinement method without FFT approximation; two cycles only)
NW-NS-2 (fast; progressive method without the FFT approximation)
NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm)
Parameters
:
Scoring matrix (for amino acid sequences):
BLOSUM30
BLOSUM45
BLOSUM62
BLOSUM80
JTT100
JTT200
Gap opening penalty:
(1.0-3.0)
Offset value:
(0.0-1.0; functions like gap extension penalty)
Output format
:
fasta
clustal
Output order
:
Same as input
Aligned
Output tree
:
Guide tree is output
Execute
