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sequences. It is advisable to keep a copy of the original
alignment. When performing this procedure the order in
which unaligned sequences are added to the profile can impact
the final alignment.
References
1. Sievers F, Wilm A, Dineen D et al (2011) Fast,
scalable generation of high-quality protein mul-
tiple sequence alignments using Clustal Omega.
Mol Syst Biol 7:539. doi: 10.1038/msb.2011.75
2. Higgins DG, Sharp PM (1988) CLUSTAL:
a package for performing multiple sequence
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Bioinformatics 23:2947-2948
4. Blackshields G, Sievers F, Shi W et al (2010)
Sequence embedding for fast construction of
guide trees for multiple sequence alignment.
Algorithms Mol Biol 5:21
5. S¨ding J (2005) Protein homology detection
by HMM-HMM comparison. Bioinformatics
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6. Arthur D, Vassilvitskii S (2007) k-means++: the
advantages of careful seeding. Proceedings of
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7. Edgar RC (2004) MUSCLE: multiple sequence
alignment with high accuracy and high through-
put. Nucleic Acids Res 32:1792-1797
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