Bio.Sequence

# Data structures etc (Bio.Sequence.SeqData)

data Sequence t
data Unknown
type Offset
type SeqData
type Qual
type QualData

## Accessor functions

seqlength
seqlabel
seqheader
seqdata
seqqual
(!)
appendHeader
setHeader

## Converting to and from String.

fromStr
toStr

## Nucleotide functionality.

compl
revcompl
revcompl'
data Nuc
castToNuc

## Protein sequence functionality

data Amino
translate
fromIUPAC
toIUPAC
castToAmino

# File formats

## The Fasta file format (Bio.Sequence.Fasta)

readFasta
hReadFasta
writeFasta
hWriteFasta

## Quality data

readQual
writeQual
hWriteQual
readFastaQual
writeFastaQual
hWriteFastaQual

## The FastQ format (Bio.Sequence.FastQ)

readFastQ
writeFastQ
hReadFastQ
hWriteFastQ

## The phd file format (Bio.Sequence.Phd)

readPhd
hReadPhd

## TwoBit file format support (Bio.Seqeunce.TwoBit)

decode2Bit
read2Bit
hRead2Bit

# Hashing functionality (Bio.Sequence.HashWord)

data HashF k
contigous
rcontig
rcpacked

# Entropy calculations

class KWords s
entropy