Phylogenetic inference methods

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. 

Phylogenetic inference methods can be broken into two categories, those that create trees based on genetic distances among taxa and those that create trees based on presence of shared character states (Felsenstein 1988, Swofford and Olsen 1990). Distance-based methods could be subdivided into... 

Phylogenetic analysis is the means of inferring or estimating evolutionary relationships. Nucleotide sequences of DNA or RNA and amino acid sequences of proteins are the most popular data used to construct phylogenetic trees. Methods of phylogenetic analysis using sequence data are introduced and performed with a software package, PHYLIP locally and online. 

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... 

DeQueiroz, K. and Poe, S., Philosophy and phylogenetic inference a comparison of likelihood and parsimony methods in the context of Karl Popper s writings on corroboration, Syst. Biol, 50, 305-321, 2001. 

The method of maximum likelihood is the standard estimation procedure in statistical inference. Whether one looks at the inference problem from the point of view of classical repeated-sampling theory or Bayesian theory or straightforward likelihood theory, maximizing the likelihood emerges as the preferred procedure. There really is no dispute about this in regular estimation problems, and phylogenetic inference does seem to be unexceptional from a statistical point of view, even though it took a little while for the initial difficulties in the application of maximum likelihood to be sorted out. This was mainly done by Felsenstein (1968) and Thompson (1974) in their Ph.D. dissertations and subsequent publications. 

Cladistics Method of classification employing genealogies alone in inferring phylogenetic relationships among organisms (see also Phylogeny). 

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