Bioinformatics Links Directory : Phylogeny Reconstruction

This section contains links to tools and databases for phylogeny reconstruction, including taxonomy resources

ConSeq - (Found June 29, 2008 )

ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and solvent-accessible, and those of structural importance are often conserved and located in the protein core. A multiple sequence alignment is used to predict the relative solvent accessibility state and the evolutionary rate at each residue.
http://conseq.bioinfo.tau.ac.il/

FGF - (Found June 29, 2008 )

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (kaks calculations).
http://fgf.genomics.org.cn/service/index.jsp

JEvTrace - (Found June 29, 2008 )

Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.
http://www.cmpharm.ucsf.edu/~marcinj/JEvTrace/

MINER - (Found June 29, 2008 )

MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).
http://www.pmap.csupomona.edu/MINER/

Phydbac2 - (Found June 29, 2008 )

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.
http://igs-server.cnrs-mrs.fr/phydbac/

PhyloDome - (Found June 29, 2008 )

PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.
http://mendel.imp.univie.ac.at/PhyloDome/

ProtTest - (Found June 29, 2008 )

ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.
http://darwin.uvigo.es/software/prottest_server.html

TSEMA - (Found June 29, 2008 )

The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families.
http://pdg.cnb.uam.es/~txemago/TSEMA/