Phylogenetic inference sequence analyses

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. 

O Donnell K, Cigelnik E, Weber NS, Trappe JM Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis. Mycologia 1997 89 48-65. 

Mollaret, I., Jamieson, B.C.M., Adlard, R.D., Hugall, A., Lecointre, G., Chombard, C. and Justine, J.-L. (1 997) Phylogenetic analysis of the Monogenea and their relationships with Digenea and Eucestoda inferred from 28S rDNA sequences. Molecular and Biochemical Parasitology 90, 433 138. 

Chisholm, L.A., Morgan, J.A.T., Adlard, R.D. and Whittington, I.D. (2001) Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences. International Journal for Parasitology 31, 1 537-1547. 

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. 

Procedures involved in the analysis of rRNA sequence data for inferring phylogenetic relationships have been extensively discussed.24,25 A critical prerequisite is that sequence alignments be carefully examined by reference to rRNA secondary structure.23,26... 

Fig. 5. Phylogenetic analysis of NRF family amino acid sequences. The amino acid sequences of known or predicted members of the NRF family in zebrafish and pufferfish were obtained from the GenBank or genome databases and aligned with the human NRF family sequences. The tree was inferred using maximum parsimony within PAUP 4b 10. The results illustrate the conservation of NRF proteins in mammals and fish as well as the additional diversity in NRF3 forms present in pufferfish. Danio rerio (Dr), Takifugu (Fugu) rubripes (Fr), Homo sapiens (Hs).

This brief guide to phylogenetic analysis has several objectives. First, a conceptual approach that describes some of the most important principles underlying the most widely and easily applied methods of phylogenetic analyses of biological sequences and their interpretation will be introduced. The aim is to show that practical phylogenetic analysis should be conceived as a search for a correct model, as much as a search for the correct tree. In this context, some of the particular models assumed by various popular methods and how these models might affect analysis of particular data sets will be discussed. Finally, some examples of the application of particular methods to the inferences of evolutionary history are provided. 

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