Helpful References

  This is, by necessity, a limited listing of places to start for more information.

Probes and Primers

• DeLong,E.F., G.S. Wickham, et al. (1989). "Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells." Science 243(4896): 1360-1363 [published erratum appears in Science 1989 Sep 22;245(4924):1312].
• Giovannoni,S.J., E.F. DeLong, et al. (1988). "Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells." J Bacteriol 170(2): 720-726 [published erratum appears in J Bacteriol 1988 May;170(5):2418].
• Lane,D.J. (1991). "16S/23S rRNA sequencing." In: E. Stackebrandt and M. Goodfellow (Eds.), Nucleic acid techniques in bacterial systematics, John Wiley and Sons, New York, NY, pp. 115-175.
• Lane,D.J., B. Pace, et al. (1985). "Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses." Proc. Natl. Acad. Sci. USA 82(20): 6955-6959.
• Palumbi,S.R. (1996). Chapter 7: "Nucleic Acids II: The Polymerase Chain Reaction." In: D.M. Hillis, C. Moritz and B.K. Mable (Eds.), Molecular Systematics, 2nd ed., Sinauer Associates, Sunderland, MA.
• Stahl,D. and R. Amann (1991). "Development and application of nucleic acid probes." In: E. Stackebrandt and M. Goodfellow (Eds.), Nucleic acid techniques in bacterial systematics, John Wiley and Sons, New York, NY, pp. 205-248.
• Stahl,D.A., B. Flesher, et al. (1988). "Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology." Appl Environ Microbiol 54(5): 1079-1084.
• Weisburg,W.G., S.M. Barns, et al. (1991). "16S ribosomal DNA amplification for phylogenetic study." J. Bacteriol. 173(2): 697-703.
• Wetmur,J.G. (1991). "DNA Probes: applications of the principles of nucleic acid hybridization." Critical Reviews in Biochemistry and Molecular Biology 26(3/4): 227-259.

  In your search for group-specific probes or primers you may want to look at the Oligonucleotide Probe Database: OPD and the Oligo Retrieval System (ORS). Also, the ARB package (ARB Sequence Database Tools) has a program that will search for such primers or probes.

Tree building

• "Molecular Evolution" by Wen-Hsiung Li (1997, Sinauer Associates, Sunderland, MA)
• "Molecular Systematics", 2nd ed., edited by Hillis,D.M., C. Moritz, B.K. Mable. (1996, Sinauer Associates, Sunderland, MA) ISBN: 0878932828 (paper lay-flat bdg.)
• Hillis, D. M. (1995). "Approaches for assessing phylogenetic accuracy." Syst. Biol. 44(1): 3.
• Hillis, D. M., M. W. Allard, et al. (1993). "Analysis of DNA sequence data: phylogenetic inference." Methods Enzymol 224: 456-87.
• Ludwig, W. and K. H. Schleifer (1994). "Bacterial phylogeny based on 16S and 23S rRNA sequence analysis." FEMS Microbiol. Rev. 15: 2-3.

  Some tools: ARB Sequence Database Tools, PAUP* version 4.0, PHYLIP, Phylogeny packages, Free Software in Molecular Biology for Macintosh and MS Windows computers, The BioCatalog

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