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.