The purpose of
phylogenetic analysis is to understand the past evolutionary path of organisms. Even though we will never know for certain the true phylogeny of any organism, phylogenetic analysis provides best assumptions, thereby providing a framework for various disciplines in microbiology. Due to the technological innovation of modern molecular biology and the rapid advancement in computational science, accurate inference of the phylogeny of a gene or organism seems possible in the near future. There has been a flood of nucleic acid sequence information, bioinformatic tools and phylogenetic inference methods in public domain databases, literature and worldwide web space. Phylogenetic analysis has long played a central role in basic microbiology, for example in taxonomy and ecology. In addition, more recently emerging fields of microbiology, including comparative genomics and phylogenomics, require substantial knowledge and understanding of phylogenetic analysis and computational skills to handle the large-scale data involved. Methods of phylogenetic analysis and relevant computer software tools lend accuracy, efficiency and availability to the task.
There are four steps in general
phylogenetic analysis of molecular sequences: (i) selection of a suitable molecule or molecules (phylogenetic marker), (ii) acquisition of molecular sequences, (iii) multiple sequence alignment (MSA) and (iv) phylogenetic treeing and evaluation. The first step of phylogenetic analysis is to choose a suitable homologous part of the genomes to be compared. Mechanisms of molecular evolution include mutations, duplication of genes, reorganization of genomes, and genetic exchanges such as recombination, reassortment and lateral gene transfer. Although all of this information can be used to infer phylogenetic relationships of genes or organisms, information on mutations, including substitution, insertion, and deletion, is most frequently used in phylogeny reconstruction. The aim is to infer a correct organismal phylogeny, using orthologous genetic loci, in which common ancestry of two sequences can be traced back to a speciation event. Phylogeny using homologous genetic loci derived by gene duplication (paralogy) or related through lateral gene transfer (xenology), cannot reflect evolutionary history of organisms.
Once DNA sequence data are generated, they are subjected to a multiple sequence alignment process. This involves finding homologous sites, that is, positions derived from the same ancestral organism in the molecules under study. A set of sequences can be aligned with another by introducing "alignment gaps" (known in brief as "gaps"). In general, multiple sequence alignment starts by aligning a pair of sequences (pairwise alignment), and is then expanded to multiple sequences using various algorithms.
Many algorithms and computer programs have been developed in the last few decades for multiple sequence alignment, but the original Clustal series programs are still most widely used and produce reasonably good quality MSA for small data sets. For a large dataset, such as massive pyrosequencing reads, the MUSCLE program can generate good compromise between accuracy and speed. The MAFFT program utilizes several different algorithmic approaches and can be used for either small or very large datasets. There are also other computer programs developed for general multiple sequence alignment, but the above three have been most popular and are routinely used in publications in various microbiological disciplines
read more ...from Molecular Phylogeny of Microorganisms by Aharon Oren and R. Thane Papke (2010)ReferencesLabels: Clustal, Comparative genomics, MAFFT, Multiple sequence alignment, MUSCLE, Phylogenetic analysis, Phylogenetic inference methods, Phylogenetic marker, Phylogenetic tree, Phylogenomics, Phylogeny of a gene