This is obvious when we see the discrepancies between the results from bioinformatics and the accepted taxonomies produced by biologists, and the high confidence measures that bioinformatics has tried to attach to their results. The state of testing of PTMS is far from satisfactory. Ĭomputing phylogenies is ubiquitous, and not only of academic interest, but also quite practical: selecting model organisms, tracing disease, finding vectors, finding suitable defenses to new viruses, maximizing diversity for species conservation, tracing ancestry and population movements and many other problems are solved with the aid of good phylogenetic trees. Felsenstein deserves special mention for his many contributions summarized in his book. Of the many people who have contributed to this field, J. By PTMS we will understand methods which build a phylogenetic tree based solely on sequences, either coding DNA or amino acids. Phylogenetic tree reconstruction from molecular sequences (PTMS) was first suggested by Emile Zuckerkandl and Linus Pauling and is now one of the major tools in the arsenal of bioinformatics. We also think that these measures of quality of trees will motivate the design of new PTMSs as it is now easier to evaluate them with certainty. It is also clear that there is a difference between Metazoa and the rest, which points out to evolution leaving different molecular traces. This comparison also allows us to rank different components of the tree building methods, like MSAs, substitution matrices, ML tree builders, distance methods, etc. The big surprise of the evaluation is that the maximum likelihood methods do not score well, minimal evolution distance methods over MSA-induced alignments score consistently better. The correlation between the two measures is remarkably high, which supports both measures simultaneously. We consider the NCBI taxonomic classification and their derived topologies as the most accepted biological consensus on phylogenies, which are also available in electronic form. The second result is the comparison of the trees against trees derived from accepted taxonomies, the Taxon measure. This new measure, called the Intra measure, is very consistent between different groups of species and strong in the sense that it separates the methods with high confidence. Our first result is a statistically significant evaluation of 176 PTMSs done by comparing trees derived from 193138 orthologous groups of proteins using a new measure of quality between trees. These are methods which base their construction solely on sequences, coding DNA or amino acids. We analyze phylogenetic tree building methods from molecular sequences (PTMS).
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