Bioinformatics and Functional Genomics

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Chapter 11: Molecular phylogeny and evolution


Web resources from Chapter 11
Website URL
Deep Green http://ucjeps.berkeley.edu/bryolab/greenplantpage.html
The Ribosomal Database http://rdp.cme.msu.edu/html/
The Felsenstein software links http://evolution.genetics.washington.edu/phylip/software.html
PHYLIP http://evolution.genetics.washington.edu/phylip/general.html
The HIV Sequence Database at the Los Alamos National Laboratory http://hiv-web.lanl.gov/content/hiv-db/TREE_TUTORIAL/Tree-tutorial.html
Sinauer Associates (PAUP) http://www.sinauer.com
PAUP http://paup.csit.fsu.edu/index.html
TREE-PUZZLE http://www.tree-puzzle.de/

 

Tables

Table 11-3. ReadSeq servers available on the internet; there are many others.
Source
Baylor College of Medicine
Center for Information Technology, National Institutes of Health
Pasteur Institute
European Bioinformatics Institute
 
Web Resources
URL Description
CLUSTALW  
ReadSeq Converts Sequence Formats using ReadSeq
The Cretaceous Period  
Dinofish Coelocanth page
W. Ford Doolittle  
How Old is Old?  
Athro Limited  
Diana Leigh Lipscomb
 
UCMP Exhibit Halls-Evolution Wing  
Carl Linnaeus (1707-1778)  
Journey into Phylogenetic Systems  
Evolutionary Biology Group University of Oxford evolutionary biology, molecular evolution and phylogenetic epidemiology
Origin of Life web site University of Glasgow  
Origins of Life  
The Paleobiology Database Paleobiology database
PHYLIP homepage  
Phylogeny programs  
Sinauer Associates, Inc.  
Kurt Stuber Library List of historic and classical biology books
The Tree of Life-Panspermia Project  
Workshop on evolution lectures Marine Biology Lab
The Tree of Life Website  
Ernst Haeckel (1834-1919)  
BioEdit  
tree drawing software  
PAUP  
PAUP Phylogenetic Analysis Using Parsimony (and Other Methods) -software
Phylogeny programs  
Treebase general phylogeny information
NCBI taxonomy homepage  
Phylogeny Programs Listing Lists 113 phylogeny packages
More Phylogeny Programs lists almost as many packages
The Tree of Life Project at the U. of Arizona
Dr. Stuart Ray's phylogeny links  
Glossary of phylogeny terms  
Introduction to cladistics  
 
 

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