Question: Looking For Review Articles/Tutorials About Understanding And Interpreting Phylogenetic Trees
2
gravatar for aravind ramesh
7.4 years ago by
India
aravind ramesh530 wrote:

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

• 3.8k views
ADD COMMENTlink modified 7.4 years ago by Josh Herr5.7k • written 7.4 years ago by aravind ramesh530
8
gravatar for Zev.Kronenberg
7.4 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Zev.Kronenberg11k
1

+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.

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by Josh Herr5.7k
1

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

ADD REPLYlink written 7.4 years ago by Zev.Kronenberg11k

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

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by aravind ramesh530

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

ADD REPLYlink written 7.4 years ago by Zev.Kronenberg11k
5
gravatar for Khader Shameer
7.4 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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

ADD COMMENTlink written 7.4 years ago by Khader Shameer18k
5
gravatar for neal.platt
7.4 years ago by
neal.platt230
United States
neal.platt230 wrote:

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.

ADD COMMENTlink written 7.4 years ago by neal.platt230

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

ADD REPLYlink modified 7.4 years ago • written 7.4 years ago by Josh Herr5.7k
5
gravatar for Josh Herr
7.4 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

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.

ADD COMMENTlink modified 6.4 years ago • written 7.4 years ago by Josh Herr5.7k
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