Phylogenetic Trees Made Easy: A How-To Manual

Phylogenetic Trees Made Easy helps beginners 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 may be familiar with phylogenetic theory but are unfamiliar with the tools used to apply that theory. The reader is led, step by step, through identifying sequences that are homologous to a sequence of interest, downloading these sequences from databases, creating multiple alignments, and using several different methods to construct trees. “Learn More” boxes present background on the various concepts and methods, and an accompanying CD and Website provide files needed for working through the tutorials in the text. Key changes to the Second Edition * discussion and screen shots updated to reflect current software versions
* all software discussed available for Macintosh, PC, and UNIX platforms
* detailed discussion of PAUP* for both Macintosh and Windows
* inclusion of PHYLIP as an alternative to PAUP*
* addition of “Advanced Topics,” including constructing deep phylogenies from protein structure comparisons, ancestral sequence reconstruction, and measuring positive selection as evidence of adaptive evolution Every copy of the Second Edition includes a CD with current Windows and Macintosh beta versions of PAUP*. These time-limited versions will allow semester-length use of this popular software, giving students hands-on experience in tree-building as they work through the text.