Phylogenetic inference

Sankoff, D., Leduc, G., Antoine, N. et al. (1992) Gene order comparisons for phylogenetic inference evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences of the United States of America, 89 (14), 6575-6579. 

Blair, D. and Barker, S.C. (1 993) Affinities of the Cyliauchenidae utility of the 1 8S rRNA gene for phylogenetic inference in the Digenea (Platyhelminthes). International Journal for Parasitology 23, 527-532. 

Hillis, D.M. and Dixon, M.T. (1991) Ribosomal DNA molecular evolution and phylogenetic inference. Quarterly Review of Biology 66, 41 1-453. 

Sequence data can be analyzed for (a) Sequence characteristics by knowledge-based sequence analysis, (b) Similarity search by pairwise sequence comparison, (c) Multiple sequence alignment, (d) Sequence motif discovery in multiple alignment, and (e) phylogenetic inference. 

Phylip (Phylogenetic Inference Package) is a software package comprising about 30 command-line programs that cover almost any aspect of phylogenetic analysis... 

In any systematic study the number of characters used to generate the phylogenetic inference needs to be maximized. At the same time homo-plasy or convergence of characters needs to be minimized. mtDNA genes for systematic studies should take both of these factors into consideration. 

If phylogenetic signal is present in a matrix of sequences, then the third step is selecting a method of phylogenetic inference. Some of the following questions must be answered to make an informed choice among the... 

Haase G, Sonntag L, Melzer-Krick B, de Hoog GS Phylogenetic inference by SSU gene analysis of members of Herpotrichiellaceae with special reference to human pathogenic species. Stud Mycol 1999 43 80-97. 

Ronquist F, Huelsenbeck JP. MRBAYES 3 Bayesian phylogenetic inference under mixed models. Bioinformaiics 2003 19 1572-1574. 

Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic inference. In Molecular Systematics 2nd Hillis DM, Moritz C, Mable BK, Eds. 407-514, 1996. 

Paradoxical as it may sound, by far the most important factor in inferring phytogenies is not the method of phylogenetic inference but the quality of the input data. The importance of data selection and in particular of the alignment process caimot be overestimated. Even the most sophisticated phylogenetic inference methods are not able to correct for erroneous input data. 

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