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Phylogenetic Example Papers:
Alves, M.J., et al. 2001.
Mitochondrial DNA variation in the highly endangered cyprinid fish
Anaecypris hispanica
: importance for conservation.
Heredity
87(Pt 4):463-473.
Basler, C.F., et al. 2001.
Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes.
PNAS
98(5):2746-2751.
Komatsu, K., et al. 2001.
Phylogenetic analysis based on 18S rRNA gene and matK gene sequences of
Panax vietnamensis
and five related species.
Planta Med
67:461-465.
Lau, D. T.-W., et al. 2001.
Authentication of medicinal
Dendrobium
species by the internal transcribed spacer of ribosomal DNA.
Planta Med
67:456-460.
Metzker, M. L., et al. 2002.
Molecular evidence of HIV-1 transmission in a criminal case.
PNAS
99(22):14292-14297.
Ou, C.-Y., et al. 1992.
Molecular epidemiology of HIV transmission in a dental practice.
Science
256(5060):1165-1171.
Pradeep Kumar, N., et al. 2002.
Genetic variability of the human filarial parasite,
Wuchereria bancrofti
in South India.
Acta Trop
82(1):67-76.
Trepanier, T.L., and R.W. Murphy. 2001.
The Coachella Valley fringe-toed lizard (
Uma inornata
): genetic diversity and phylogenetic relationships of an endangered species.
Mol Phylogenet Evol
18(3):327-334.
Vogel, G. 1998.
HIV strain analysis debuts in murder trial.
Science
282(5390): 851-853.
Phylogenetics Methods and Software:
Benton, M.J., and F.J. Ayala. 2003.
Dating the tree of life.
Science
300(5626):1698-1700.
Felsenstein, J. 1981.
Evolutionary trees from DNA sequences: a maximum likelihood approach.
J Mol Evol
17:368-376.
Felsenstein, J. 1996.
Inferring phylogenies from protein sequences by parsimony, distance and likelihood methods.
Meth Enzymol
266:418-427.
Huelsenbeck, J.P. and F. Ronquist. 2001.
MRBAYES: Bayesian inference of phylogenetic trees.
Bioinformatics
17(8):754-755.
Kumar, S., K. Tamura, and M. Nei. 2004.
MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment.
Briefings in Bioinformatics
June;5(2):150-63.
Mace, G.M., J.L. Gittleman, and A. Purvis. 2003.
Preserving the tree of life.
Science
300(5626):1707-1709.
Maddison, W. 1993. Phylogenetic interpretations of character evolution using the computer program MacClade.
J Gen Physiol
102(6):9A-10A.
Maddison, W., and D.R. Maddison. 1989.
Interactive analysis of phylogeny and character evolution using the computer program MacClade.
Folia Primatol (Basel)
53(1-4):190-202.
Marshall Graves, J.A. 2003.
The Tree of Life: view from a twig.
Science
300(5626):1621.
Pennisi, E. 2003.
Modernizing the tree of life.
Science
300(5626):1692-1697.
Remsen, J. and P. O'Grady. 2002.
Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support.
Mol Phylogenet Evol
24(2):249-264.
Ronquist, F. and J.P. Huelsenbeck. 2003.
MRBAYES 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics
19(12):1572-1574.
Phylogenetic Resources
Revised 07/22/2005