1,233
Views
2
CrossRef citations to date
0
Altmetric
Protocol

Bioinformatics analysis of large-scale viral sequences

From construction of data sets to annotation of a phylogenetic tree

Pages 97-106 | Received 29 Aug 2012, Accepted 06 Dec 2012, Published online: 01 Jan 2013

References

  • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008; 26:1135 - 45; http://dx.doi.org/10.1038/nbt1486; PMID: 18846087
  • Swofford D, Olsen G, Waddel P, Hillis DM. Phylogenetic inference. Pages in (Molecular systematics, 2nd edition (D. M. Hillis, C.Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
  • Page R, Holmes E. Molecular evolution: A phylogenetic approach. Blackwell, Osney Mead, Oxford, UK.
  • Uzzell T, Corbin KW. Fitting discrete probability distributions to evolutionary events. Science 1971; 172:1089 - 96; http://dx.doi.org/10.1126/science.172.3988.1089; PMID: 5574514
  • Jin L, Nei M. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 1990; 7:82 - 102; PMID: 2299983
  • Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 1996; 11:367 - 72; http://dx.doi.org/10.1016/0169-5347(96)10041-0; PMID: 21237881
  • Kamel AH, Ali MA, El-Nady HG, de Rougemont A, Pothier P, Belliot G. Predominance and circulation of enteric viruses in the region of Greater Cairo, Egypt. J Clin Microbiol 2009; 47:1037 - 45; http://dx.doi.org/10.1128/JCM.01381-08; PMID: 19193841
  • Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005; 21:456 - 63; http://dx.doi.org/10.1093/bioinformatics/bti191; PMID: 15608047
  • Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2007; 2:e383; http://dx.doi.org/10.1371/journal.pone.0000383; PMID: 17440619
  • Ebersberger I, Strauss S, von Haeseler A. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 2009; 9:157; http://dx.doi.org/10.1186/1471-2148-9-157; PMID: 19586527
  • Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B. OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. BMC Bioinformatics 2009; 10:219; http://dx.doi.org/10.1186/1471-2105-10-219; PMID: 19607672
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389 - 402; http://dx.doi.org/10.1093/nar/25.17.3389; PMID: 9254694