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Appendix II - A selection of biological sequence analysis software

Published online by Cambridge University Press:  05 August 2012

Tore Samuelsson
Tore Samuelsson
Affiliation:
Göteborgs Universitet, Sweden
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Genomics and Bioinformatics
An Introduction to Programming Tools for Life Scientists
 , pp. 289 - 299
Publisher: Cambridge University Press
Print publication year: 2012

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References

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Altschul, S. F. Madden, T. L. Schaffer, A. A. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 3389 CrossRefGoogle ScholarPubMed
Eddy, S. R. 1998 Profile hidden Markov models Bioinformatics 14 755 CrossRefGoogle ScholarPubMed
Edgar, R. C. 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 113 CrossRefGoogle ScholarPubMed
Felsenstein, J. 1989 PHYLIP: Phylogeny Inference Package (Version 3.2) Cladistics 5 164 Google Scholar
Felsenstein, J. 2005
Kent, W. J. 2002 BLAT: the BLAST-like alignment tool Genome Res 12 656 CrossRefGoogle ScholarPubMed
Markel, S. León, D. 2003 Sequence Analysis in a Nutshell: A Guide to Tools and Databases Farnham and Sebastopol, CA O’Reilly
Nawrocki, E. P. Kolbe, D. L. Eddy, S. R. 2009 Infernal 1.0: inference of RNA alignments Bioinformatics 25 1335 CrossRefGoogle ScholarPubMed
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Perriere, G. Gouy, M. 1996 WWW-query: an on-line retrieval system for biological sequence banks Biochimie 78 364 CrossRefGoogle ScholarPubMed
Rice, P. Longden, I. Bleasby, A. 2000 EMBOSS: the European Molecular Biology Open Software Suite Trends Genet 16 276 CrossRefGoogle ScholarPubMed
Ronquist, F. Huelsenbeck, J. P. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 CrossRefGoogle ScholarPubMed
Thompson, J. D. Gibson, T. J. Higgins, D. G. 2002 Multiple sequence alignment using ClustalW and ClustalX Curr Protoc Bioinformatics Google ScholarPubMed
Waterhouse, A. M. Procter, J. B. Martin, D. M. Clamp, M. Barton, G. J. 2009 Jalview Version 2: a multiple sequence alignment editor and analysis workbench Bioinformatics 25 1189 CrossRefGoogle ScholarPubMed

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