Abstract
The term phylogeny refers to the progression or historical development of a plant, animal, or microbial species, the tracing of such similar group having a common ancestor. Thus phylogenetic tree is a visual graphical representation of the evolutionary relationship between different organisms, showing the path through evolutionary time from a common ancestor to different descendants. Similarities and divergence among related biological sequences revealed by sequence alignment often have to be rationalized and visualized in the context of phylogenetic trees. But with the development and use of computational and an array of bioinformatics tools, the ability to analyze large data sets in practical computing times and yielding an optimal or near-optimal solutions with high probability are being possible.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Brown, D., & Sjölander, K. (2006). Functional classification using phylogenomic inference. PLoS computational biology, 2(6), e77
**ong, J. (2006). Essential bioinformatics. Cambridge University Press
Lesk, A. (2019). Introduction to bioinformatics. Oxford university press
Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., & van Sinderen, D. (2007). Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiology and molecular biology reviews, 71(3), 495–548.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of molecular biology, 215(3), 403–410
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research, 25(24), 4876–4882
Takahashi, K., & Nei, M. (2000). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Molecular biology and evolution, 17(8), 1251–1258
Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution, 4(4), 406–425
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5 c. Joseph Felsenstein
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2–approximately maximum-likelihood trees for large alignments. PloS one, 5(3), e9490
Tamura, K., Dudley, J., Nei, M., & Kumar, S. (2007). MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular biology and evolution, 24(8), 1596–1599
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Kaari, M., Joseph, J., Manikkam, R., Shamya, M., Aruni, W. (2022). Application of Bioinformatic Tools for Phylogenetic Analysis. In: Dharumadurai, D. (eds) Methods in Actinobacteriology. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1728-1_27
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1728-1_27
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1727-4
Online ISBN: 978-1-0716-1728-1
eBook Packages: Springer Protocols