I am interested in learning more in depth this topic whereby I have been already introduced and I have a limited experience.
My book "Phylogenetic Trees Made Easy: A How-to Manual" 4th Edition, 2011 was written specifically to provide an introduction to the practical aspects of phylogenetic reconstruction. It focuses on using the free program MEGA, and includes examples, tutorials and lots of screen shots. Although it is used as a supplementary text in numerous courses, it deals very little with theory and a great deal with practical application. Available at most University libraries, or for sale from Amazon.
I advise you to consult this very interesting book: 'Estimating Species Trees: Practical and Theoretical Aspects' edited by L. Lacey Knowles and Laura S. Kubatko.
I hope this would help, good reading!!
Dear Fulvio,
This a very interesting book on phylogenetics. In addition, there is a free program package (MEGA) closely linked to this book. In fact, the authors of both the book and the software are the same.
- Nei M, Kumar S (2000). "Molecular Evolution and Phylogenetics". Oxford University Press, Inc.
I hope this information can be useful for you.
Best regards and good luck !!!
We tried to summarize best (modern) practices in this open access paper:
https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers
The focus is on fungi, but I think you'll find that much of applies to the field at large.
Article Incorporating molecular data in fungal systematics: A guide ...
Dear Fulvio,
I recomendate book Evolutionary Pathways in Nature
A Phylogenetic Approach by J. Avise. 2006. Cambridge University Press
The Edinburgh Building, Cambridge cb2 2ru, UK, Published in the United States of America by Cambridge University Press, New York
This is a book about step-by-step phylogenetic reconstruction:
"Phylogenetic Trees Made Easy: A How-To Manual" 2011 Edition: Fourth
http://www.sinauer.com/phylogenetic-trees-made-easy-a-how-to-manual.html
Not a book, but a very basic practical introduction to MEGA is found here:
Hall, B. G. (2013). Building phylogenetic trees from molecular data with MEGA. Molecular Biology and Evolution 30(5), 1229-1235.
http://mbe.oxfordjournals.org/content/30/5/1229.full
My book "Phylogenetic Trees Made Easy: A How-to Manual" 4th Edition, 2011 was written specifically to provide an introduction to the practical aspects of phylogenetic reconstruction. It focuses on using the free program MEGA, and includes examples, tutorials and lots of screen shots. Although it is used as a supplementary text in numerous courses, it deals very little with theory and a great deal with practical application. Available at most University libraries, or for sale from Amazon.
I second the above recommendations. Additionally, there is plenty of information in the documentation associated to each of the phylogenetic estimation packages available online.
The best possible approach I can advise if you have time is to select a few taxa with well determined phylogenies, and download sequences for a number of different orthologue genes from sequence databases like NCBI's or ensEMBL, and try aligning them, estimating trees using different genes and different estimation methods. That will give you a feel for how different genes may tell different stories, and how the evolutionary history of certain lineages can affect the topology of the overall tree. Also, explore how gene/marker and taxon sampling influence your output.
It takes a decent amount of time and computational power, but it is fun and revealing, and might change a lot how you look at published molecular phylogenies.
In addition to the above mentioned, and if you are particularly interested in Bayesian inference, I recommend two recent books:
Bayesian Phylogenetics: Methods, Algorithms, and Applications by Ming-Hui Chen, Lynn Kuo, Paul O. Lewis (2014)
Bayesian evolutionary analysis with BEAST 2 by Alexei J. Drummond and Remco R. Bouckaert (2014)
This last one has many practical examples for the widely used BEAST2 and is freely available from http://beast2.org/book.html
this is very nice book in study of Phylogeny
"The Phylogenetic Handbook
A Practical Approach to Phylogenetic
Analysis and Hypothesis Testing"
Second Edition, 2009
Edited by
Philippe Lemey
Katholieke Universiteit Leuven, Belgium
Marco Salemi
University of Florida, Gainesville, USA
Anne-Mieke Vandamme
Katholieke Universiteit Leuven, Belgium
CAMBRIDGE UNIVERSITY PRESS
Phylogenetic Trees Made Easy: A How-To Manual" 2011 Edition: Fourth
http://www.sinauer.com/phylogenetic-trees-made-easy-a-how-to-manual.html
Molecular Evolution and phylogenetics. Nei & Kumar
or previously mentioned
Phylogenetic Trees Made Easy: A How-To Manual"
- Badges
- Science topic
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics