Phylogeny inference

Felsenstein, J. (1989). Phylip phylogeny inference package (version 3.2). Cladistics 5, 164-166. 

Wink, M. and Mohamed, G. 1. A. 2003. Evolution of chemical defense traits in the Leguminosae Mapping of distribution patterns of secondary metabolities on a molecular phylogeny inferred from nucleotide sequences of the rbcL gene. Biochemical Systematics and Ecology, 31 8 897-917. 

Phylogenies inferred from mitochondrial gene orders - a cautionary tale from the parasitic flatworms. Molecular Biology and Evolution 1 7, 1 123-1 125. 

Litvaitis, M. and Rhode, K. (1999) A molecular test of platyhelminth phylogeny inferences from partial 28S rDNA sequences. Invertebrate Biology 1 18, 42-56. 

Rehner, S. A., and Buckley, E. (2005). A Beauveria phylogeny inferred from nuclear ITS and EFl-a sequences evidence for cryptic diversification and links to Cordyceps tclcomorphs. Mycologia, 97, 84-98. 

Felsenstein J (1999) PHYLIP - Phylogeny inference package, version 3.6. University of Washington, Seattle... 

J. Felsenstein, PHYLIP (Phylogeny Inference Package), Version 3.5, Manual, University of Washington, Seattle, 1993. 

Phylogenies inferred from the amino-acid identities also bear this out (Fig. 1), the root of the archaeal subtree being closer to the (present) eucaryal root than to the bacterial root, and more evidently so in the case of the EF-la trees. Furthermore, both the EF-la/EF-Tu and the EF-2/EF-G trees confirm the deep subdivision of the archaea into two major branches constituting the kingdoms of Crenarchaeota and Euryarchaeota[52]. 

Phylogeny inference from antibiotic sensitivity spectra... 

Hedges S.B., Moberg K.D., Maxson L.R. (1990). Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. Mol. Biol. Evol. 7 607-633. 

Zardoya, R. et al.. Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences, J. Mol. Biol. 41, 637, 1995. 

The relevance of distance- and maximum-likelihood methods for phylogeny inference... 

Mathews, S. and Donoghue, M. J. (1999). Ihe root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science, 286,947-950. 

Soltis, D. E., Soltis, P. S., Chase, M. W. et al. (2000). Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of theLinnean Society, 133,381-461. 

Saito, M. (1998) Brachiopod phylogeny inferred from mitochondrial COI sequences. Doctoral Thesis, University of Tokyo. 

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