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Table 1 Character state coding used by BMGE

From: BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

Nucleotide

1-letter code

  

Adenosine

A

  

Guanine

G

  

Cytosine

C

  

Thymine

T

  

Degenerated nucleotide

1-letter code

Meaning

 

Methyl

M

A or C

 

Purine

R

A or G

 

Weak (3 H bonds)

W

A or T

 

Strong (3 H bonds)

S

C or G

 

Pyrimidine

Y

C or T

 

Keto

K

G or T

 
 

B

not A

 
 

D

not C

 
 

H

not G

 
 

V

not T

 

Any

N or X

one of the 4 nucleotides

 

Amino acid

1-letter code

 

Degenerated codon

3-letter code

Alanine

A

 

GCX

Arginine

R

 

MGX

Asparagine

N

 

AAY

Aspartic acid

D

 

GAY

Cysteine

C

 

TGY

Glutamine

Q

 

CAR

Glutamic acid

E

 

GAR

Glycine

G

 

GGX

Histidine

H

 

CAY

Isoleucine

I

 

ATH

Leucine

L

 

YTX

Lysine

K

 

AAR

Methionine

M

 

ATG

Phenylalaline

F

 

TTY

Proline

P

 

CCX

Serine

S

 

WSX

Threonine

T

 

ACX

Tryptophan

W

 

TGG

Thyrosine

Y

 

TAY

Valine

V

 

GTX

Degenerated amino acid

1-letter code

Meaning

Degenerated codon

3-letter code

Aspartate

B

N or D

RAY

Glutamate

Z

Q or E

SAR

Any

X

one of the 20 amino acids

XXX

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BMC Ecology and Evolution

ISSN: 2730-7182

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