ISBN : 9781605357102
Phylogenetic Trees Made Easy, Fifth Edition helps the reader get started in creating phylogenetic trees from protein or nucleic acid sequence data. Although aimed at molecular and cell biologists, who may not be familiar with phylogenetic or evolutionary theory, it also serves students who have a theoretical understanding of phylogenetics but need guidance in transitioning to a practical application of the methodology. The reader is led, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. "Learn More" boxes present background on the various concepts and methods.
New to this Edition:
- The release of this edition was prompted by the development of a new version of the phylogenetic software MEGA. MEGA7 has several capabilities that were not present in MEGA5.
- Three new chapters (Minimum Spanning Trees; Time Trees; and Estimating Phylogenetic Trees from Whole Genome Sequences) address important advanced topics.
- The chapter on Bayesian Inference is now illustrated using the program BEAST, a WYSIWYG program with a familiar application environment.
- Three new Appendices discuss text editors, the many command-line programs that are available, and facilitating the installation of those programs in the Windows, Mac, and Linux environments.
- New screen shots throughout show the current versions of all software. These illustrations are in full color, enabling readers to more easily identify elements in which color plays an important informational role.
- This edition is organized into 19 (versus 16) chapters, to better isolate important topics.
1 Read Me First!
2 Tutorial: Estimate a Tree
3 Acquiring the Sequences
4 Aligning the Sequences
5 Major Methods for Estimating Phylogenetic Trees
6 Neighbor Joining Trees
7 Drawing Phylogenetic Trees
9 Maximum Likelihood
10 Bayesian Inference of Trees Using BEAST
11 Which Method Should You Use?
12 Working with Various Computer Platforms
13 Phylogenetic Networks
14 Minimum Spanning Trees
15 Time Trees
16 Reconstructing Ancestral Sequences
17 Detecting Adaptive Evolution
18 Estimating Phylogenetic Trees from Whole Genome Sequences
19 Some Final Advice: Learn to Program