Methods and Programs for Calculation of Phylogenetic Relationships from Molecular Sequences
Jongsik Chun and Soon Gyu Hong
from: Molecular Phylogeny of Microorganisms (Edited by: Aharon Oren and R. Thane Papke). Caister Academic Press, U.K. (2010)
Abstract
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. In this chapter we will review major steps in phylogenetic analysis and introduce relevant computer software tools with respect to their accuracy, efficiency and availability read more ...
