Practical Course on Multiple Sequence Alignment - CNB - Protein ...

Choosing the right MSA software
Given the multitude of choices, it can be difficult for a user of multiple
alignment software to understand the situations in which a particular
alignment tool is or is not appropriate. When aligning a small number (40%), most
modern alignment programs will have no difficulty in returning a correct
multiple sequence alignment, and no special consideration is needed. When all
of these conditions do not hold, however, choosing the appropriate tools and
configuration, while keeping in mind the tradeoff between accuracy and
computational cost, can be difficult. You can find a list of currently popular
alignment software (see Table 2) and advice on tool selection (see Fig. 5).
For more advanced discussion on software selection see (Do & Katoh, 2008).
Figure 5: Decision tree for choosing the right MSA program.
Alignment visualization and editing
Once an alignment has been generated, visualization tools allow manual
identification of regions with reliably predicted homology; many of these tools
also allow for interactive alignment editing.
For alignments of sequences with low similarity, post-processing is extremely
important as most regions in a low-identity alignment will not be reliably
alignable.
Visual inspection of an alignment and subsequent identification of potentially
mis-aligned regions can be greatly helped using hints provided by software
that highlight such regions. Typically, high confidence aligned regions can be
identified by looking for groups of residues with strongly conserved
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