Phylogeny
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Berkeley Phylogenomics Group provides tools for phylogenomic analysis of protein or gene function is a form of functional genomics, designed to improve the accuracy of predicted molecular function, by integrating evolutionary tree construction and analysis in the annotation pipeline. Combines phylogenomic approaches with protein structure prediction, to elucidate the correlation between changes in protein structure and changes in molecular function. Includes tools Phylobuilder, Muscle, FlowerPower, SCI-PHY, SATCHMO, Predict structure, and TreeNotator.
TreeTop server at the A.N.Belozersky Institute produces putative phylogenetic trees prediction from multiple sequence alignments by cluster and topological algorithms. Outputs tress as slanted cladogram, rectangular cladogram, phylogram, or unrooted.
Tree of Life
The Tree of Life is a collaborative web project, produced by biologists from around the world. On more than 2600 World Wide Web pages, the Tree of Life provides information about the diversity of organisms on Earth, their history, and characteristics.
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TreeGen Tree generation from distance data.
SplitsTree
Distance-based phylogeny reconstruction based on split-decomposition. SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences. See also the original side of splitstree at the University of Tuebingen.
ROSE Random-model Of Sequence Evolution. ROSE implements a new probabilistic model of RNA-, DNA-, or protein-sequence evolution.
Phydbac
Phylogenomic display of bacterial genes: an interactive resource for the annotation of bacterial genomes. 
ParSeq
Searching motifs with structural and biochemical properties. Searches for variable motifs such as protein-binding sites or promoter regions are more complex than the search for casual motifs. For example, in amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions that represent proteins with a special function, because the function depends on biochemical properties of individual amino acids (such as polarity or hydrophobicity). Pure string matching programs are not able to find these motifs hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical properties, an approximate search mechanism and a stepwise creation of the motif description by allowing to search on previously obtained results.
Galaxie
CGI scripts for sequence identification through automated phylogenetic analysis. The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable.
Services - MultiAlign: Multiple Sequence Alignment Tools A multiple-sequence alignment program that also includes distance matrix methods for inferring trees.
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GRIMM - Genome Rearrangement Algorithms A tool for constructing phylogenies based on gene order for unichromosomal and multichromosomal genomes
