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Home > Extras > Bioinformatics For Dummies® Bonus Material
Bioinformatics For Dummies® Bonus Material
By: Jean-Michel Claverie Ph.D., Cedric Notredame Ph.D.
 

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Chapter 13: Building Phylogenetic Trees

Chapter 13 images

Online sites for making phylogenetic trees

URL Description
www.ebi.ac.uk/clustalw/ Use ClustalW to build multiple alignments and compute NJ trees.
www.genebee.msu.ru/clustal/basic.html The Genebee server can produce genuine phylogenetic trees in one step.
www.es.embnet.org/Doc/jalview/ help.html You can use Jalview to produce NJ trees. A very powerful tool that can combine alignment edition with tree computation.
sdmc.krdl.org.sg:8080/~lxzhang/phylip/ A Web interface for Phylip. Many other phylogeny-related programs are also available online at the Pasteur site.
bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html A Web interface for Phylip.
www.genebee.msu.ru/services/phtree_reduced.html Very powerful interface for a new tree reconstruction method.

Generic phylogenetic resources on the Internet

URL Description
evolution.genetics.washington.edu/phylip/software.html Joe Felsenstein's pages, where Phylip lives; it's also one of the most extensive collections of resources available. Truly a legendary site!
www.ucmp.berkeley.edu/subway/phylo/phylosoft.html A very complete list of phylogeny resources.
paup.csit.fsu.edu/index.html The home of PAUP, the other legendary phylogeny package. Although PAUP is a commercial package, it's reasonably priced and worth every penny, according to specialists.
www.ncbi.nlm.nih.gov/About/primer/phylo.html The NCBI primer on phylogeny.
www.techfak.uni-bielefeld.de/bcd/Curric/MathAn/mathan.html A high-quality course on tree reconstruction methods.

Collections of orthologous sequences

URL Description
www.ncbi.nlm.nih.gov/COG/ Clusters of orthologous sequences maintained by the NCBI. Each cluster contains proteins from bacterial genomes.
pbil.univ-lyon1.fr/databases/hovergen.html A collection of orthologous vertebrate genes.
pbil.univ-lyon1.fr/databases/hobacgen.html A collection of orthologous bacterial genes.
systers.molgen.mpg.de Another collection of homologous sequences.
rdp.cme.msu.edu/html/
rrna.uia.ac.be 		Two extensive collections of ribosomal RNA sequences, which are very useful for classifying new organisms, and come with appropriate phylogenetic tools.

 
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