Table 5. Phylogenetic Resources
Sites for Making Phylogenetic Trees
Program Website Comments
ClustalW Builds alignments, computes NJ trees, bootstraps
ClustalW Produces genuine phylogenetic trees in one step
Phylip Server for phylogeny related programs
Phylogenetic Resources
Program Website Comments
List of more than 200 phylogeny programs and servers
Taxonomy Taxonomic classes at NCBI
Collections of Orthologous Genes
Program Website Comments
HomoloGene Gene orthologs; pairwise comparison of organisms
COG Clusters of orthologous groups of proteins
EGO Eukaryotic gene orthologs. Pairwise comparisons
Hovergen Homologous vertebrate genes database
Program Website Comments

Free software. Highly recommended
HyperTree Handles large trees. Supports circular and linear trees
ClustalX (PC) Free software. Computes NJ trees, bootstraps