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namespace ost { namespace seq {
/*!
\page module_seq The Sequence Module
\section seq_mod The seq Module
In bioinformatics, biological sequence data occurs in 3 different ways: As a
single sequences, lists of sequences and in form of sequence alignments. These
3 ways of looking at sequence data is encoded in the seq module by 3 different
classes. The simplest of this classes is the SequenceHandle, representing a
single sequence. To represent a list of sequences, the module provides the
SequenceList class and alignment-based data is represented by AlignmentHandle.
The main difference between the SequenceList and AlignmentHandle classes is,
that the sequence list classes are mainly used sequence-wise, while in
Alignments one often looks at an aligned column. This results in a drastically
different interface, even if both of them work on lists of sequences.
\subsection seq_io Sequence IO
Sequence IO is dealt-with in the io module. To load single sequences, use
ost::io::LoadSequence(), sequence lists use ost::io::LoadSequenceList(),
and alignments use ost::io::LoadAlignment().
\subsection seq_conv Converting between alignments and sequence lists
AlignmentHandle::GetSequences() provides read-only access to a sequence-based
view. To create an alignment from a list of sequences, use
\ref AlignmentFromSequenceList(const SequenceList&). This method will fail when
not all of the sequences have the same length. If the sequence lengths differ,
they have to be padded accordingly.
*/
}}
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