Table 5. Phylogenetic Resources
Sites for Making Phylogenetic Trees
Program Website Comments
ClustalW http://www.ebi.ac.uk/clustalw/ Builds alignments, computes NJ trees, bootstraps
ClustalW http://www.genebee.msu.ru/clustal/basic.html Produces genuine phylogenetic trees in one step
Phylip http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html Server for phylogeny related programs
Phylogenetic Resources
Program Website Comments
Phylogeny http://evolution.genetics.washington.edu/phylip/software.html
 
List of more than 200 phylogeny programs and servers
Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ Taxonomic classes at NCBI
Collections of Orthologous Genes
Program Website Comments
HomoloGene http://www.ncbi.nlm.nih.gov/HomoloGene/ Gene orthologs; pairwise comparison of organisms
COG http://www.ncbi.nlm.nih.gov/COG/ Clusters of orthologous groups of proteins
EGO http://www.tigr.org/tdb/tgi/ego/ Eukaryotic gene orthologs. Pairwise comparisons
Hovergen http://pbil.univ-lyon1.fr/databases/hovergen.html Homologous vertebrate genes database
Software
Program Website Comments
Treeview http://taxonomy.zoology.gla.ac.uk/rod/treeview/treeview.html

 
Free software. Highly recommended
HyperTree http://198.202.68.14/tools/HyperTree.html Handles large trees. Supports circular and linear trees
ClustalX (PC) http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html Free software. Computes NJ trees, bootstraps