NGPhylogeny.fr

Input data

MAFFT

Data type

Auto detection Nucleic acids Amino acids

MAFFT flavour

auto fftns fftnsi nwns nwnsi einsi ginsi linsi qinsi xinsi Custom Parameters

Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section.

Distance method

Shared 6mers distance (fastest)

Global alignment (Needleman-Wunsch)

Local alignment (Smith-Waterman)

Local, affine gap cost

Distance method must be chosen regarding your data

Guide tree is built this number of times in the progressive stage.

Valid with 6mer distance

Maximum number of iterations

1000 for maximum quality

Gap extend penalty

Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps

Gap opening penalty

1.53 default value

Direction of nucleotide sequences

adjust direction

do not adjust direction

Generate reverse complement sequences, as necessary, and align them together with the remaining sequences

Matrix selection

No matrix

BLOSUM

PAM

Usefull only for amino acids

Coefficient of the BLOSUM matrix

30

45

62

80

Coefficient of the PAM matrix

Reorder output?

Display alignment tree ?

Output format

FASTA ClustalW Phylip

BMGE

Sequence Coding

Auto detect DNA AA Codon

matrix

Name of the PAM matrix [ 1-500 ]

matrix

Estimated matrix BLOSUM

30 35 40 45 50 55 60 62 65 70 75 80 85 90 95

matrix

Estimated matrix BLOSUM

30 35 40 45 50 55 60 62 65 70 75 80 85 90 95

Estimated matrix BLOSUM (if protein)

30 35 40 45 50 55 60 62 65 70 75 80 85 90 95

Name of the PAM matrix [ 1-500 ] (if dna)

Estimated matrix BLOSUM (if protein)

30 35 40 45 50 55 60 62 65 70 75 80 85 90 95

Name of the PAM matrix [ 1-500 ] (if dna)

Sliding Windows Size

sliding window size (must be odd; ranges from 1 to alignment length; if set to 1, then entropy-like values are not smoothed; default: 3)

Maximum entropy threshold

Gap Rate cut-off [ 0-1 ]

Minimum Block Size

Newick Display

Display scale bar

Unit name scale

Leaf font

Leaf font-size

Branch support

Display branch support Hide branch support

color

font-size

move

Branch length

Display branch length Hide branch length

color

font-size

move

SVG Tree width (px)

Draw a radial tree

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