AlphabetFromString converts the alphabet name to its code If the alphabet name is not known, returns align.UNKNOWN.

Complement sequence.

EqualOrCompatible returns true if the two nucleotides are identical or if they are compatible in case they are ambigous.

GenAllPossibleCodons generates all possible codons given the 3 nucleotides in arguments Multiple codons may exist if IUPAC code is employed (R=A|G, etc.).

Returns the index of each nts 0=A 1=C 2=G 3=T */.

NewAlign initializes a new alignment.

NewCountProfile initializes a new Profile with nil attributes.

NewCountProfileFromAlignment initializes a new CountProfile using an input alignment.

Returns the index of each nts A=0 C=1 G=2 T=3 */.

Returns the int code of the given nucleotide.

NtIUPACDifference returns the cost of the difference between the two potentially ambiguous nucleotides.

PossibleNtIUPAC returns the possible meaning of the given iupac nucleotide Ex: NT_B : {NT_C, NT_G, NT_T} */.

RandomAlignment generates a random alignment with a given alphabet length and number of sequences.

Reverses a sequence.

Amino acid sequence alphabet.

Could be both.

Invertebrate mitochondrial genetic code.

Standard genetic code.

Vertebrate mitochondrial genetic code.

GAP, *, etc;?.

Nucleotid sequence alphabet.

Same strong group.

All characters in a position are the same.

None of the above values.

Same weak group.

Normalization by aa/nt frequency in data.

Normalization by freq in the site.

Normalization like LOGO : v(site)=freq*(log2(alphabet)-H(site)-pseudocount.

No normalization.

Normalization by uniform frequency.

Unkown alphabet.

AlignChannel is used for iterating over alignments.

CountProfile represents a simple view of an alignment and stores the number of occurences of each characters at each position of an alignment.

Alignment represents a set of aligned sequences (multiple Sequence Alignment).

* If SetTranslate(true): align all sequences to the given ORF and trims sequences to the start position If orf is nil, searches for the longest ORF (in 3 or 6 phases depending on reverse arg) in all sequences To do so, Phase() will: 1.

SeqBag represents a set of unaligned sequences.