All
characters translations are defined in terms of the basic alphabet:A,C,G,T.
Note:This table is identical
to PHYLIP's translation table.
Character |
Translation |
A |
Adenine |
C |
Cytosine |
G |
Guanine |
T |
Thymine |
U |
Uracil, by default translated
to T. |
B |
C, G or T |
D |
A,G or T |
H |
A,C or T |
K |
G or T |
M |
A or C |
R |
A or G |
S |
C or G |
V |
A, C or G |
W |
A or T |
Y |
C ot T |
N,X,? |
A,C,G or T |
- |
Skipped or A,C,G or T
(see Deletions and Ambiguities) |
. |
For sequential file formats is interpreted
as '?'. For interleaved formats singnals that '.' should be replaced
with the character at the same position in the first sequence. |
HYPHY
provides means for defining custom alphabets and translations.
In particular, HYPHY recognizes relevant NEXUS blocks.
However one must be careful with custom alphabets since they
may require model redefinitions.
|