Looking For Review Articles/Tutorials About Understanding And Interpreting Phylogenetic Trees

Question

[aravind ramesh]

I need some good and basic review articles for understanding and interpreting phylogenetic trees systematically. Any help will be appreciated.

Answer 1

[Zev.Kronenberg]

I would suggest two avenues to quickly coming up to speed in phylogenetics.

1) Checkout or buy "Inferring Phylogenies" by Joseph Felsenstein.

2) Start simulating population data using available software and examINE what the phylogenies look like under different population parameters.

[Josh Herr]

+1, This is just my opinion, but Joe Felsenstein's book is too dense and difficult for those looking to get into phylogenetics. It's THE best book on phylogenetics out there, but I've had so many students be completely confused by it. I suggest it for grad level phylogenetics courses.

[Zev.Kronenberg]

I agree. It completely depends on what the OP means by "understanding and interpreting". Taking a course is a great idea.

[aravind ramesh]

Thanx, I just found at coursera (https://www.coursera.org/course/molevol). By the way, what is "OP" in your comment ?

[Zev.Kronenberg]

Original Poster - Coursera is awesome. I am taking a Coursera course now.

Answer 2

[Khader Shameer]

Phylogeny for the faint of heart: a tutorial. PDF here.

Answer 3

[neal.platt]

It's not a review article, but the Phylogenetic Trees Made Easy book is best beginner tutorial you can get. It walks you through all the basics. I think most people can work through the book in a week or so. The third edition has ~ 200 pages. From the table of contents:

Ch. 1 - Introduction

Ch. 2 - Creating your first tree

Ch. 3 - Getting and aligning sequences

Ch. 4 - Neighbor-joining trees

Ch. 5 - Drawing phylogenetic trees

Ch. 6 - Parsimony

Ch. 7 - Maximum likelihood

Ch. 8 - Bayesian inference

Ch. 9 - Reconstructing ancestral sequences

Ch. 10 - Detection adaptive evolution

Ch. 11 - Computer platforms

It is not unreasonable to work through this book in a matter of days.

Hope that helps.

[Josh Herr]

+1, I second this suggestion, this is a great book appropriate for a phylogenetics beginner if you are creating trees.

Answer 4

[Josh Herr]

My book suggestion is a newish book, Tree Thinking, which just came out this year. I think that it's hands down the best text book for those beginning to understand phylogenetics (undergraduate level course in phylogenetics & cladistics). Reading Joe Felsenstein's book is the step after reading and fully understanding this book.