Bioinformatics Links Directory : Phylogeny Reconstruction

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

Tree of Life - (Found June 29, 2008 )

Multi-authored project attempting to represent online the entire phylogeny of life on earth.
http://phylogeny.arizona.edu/

TREE-PUZZLE - (Found June 29, 2008 )

Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method.
http://www.tree-puzzle.de/

TreeDomViewer - (Found June 29, 2008 )

TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.
http://www.bioinformatics.nl/tools/treedom

TreeJuxtaposer - (Found June 29, 2008 )

TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences.
http://olduvai.sourceforge.net/

TreeView - (Found June 29, 2008 )

Generates nice graphics of trees; reads multiple tree file formats; available for download to Mac or PC.
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

UCMP Phylogeny Wing - (Found June 29, 2008 )

"Phylogeny-Diversity of Life Through Time" is an on-line exhibit at the University of California Museum of Paleontology website. There is an introduction to phylogenetics and cladistics, and you can navigate through a very informative phylogenetic tree rooted at the three main domains of life (Archaea, Bacteria and Eukaryota). At each level of the tree there is a brief summary, and links to more information about the Fossil Record, Life History and Ecology, Systematics and...
http://www.ucmp.berkeley.edu/exhibit/phylogeny.html

PhyloBLAST - (Found June 29, 2008 )

BLAST a protein sequence, then perform automated phylogenetic analysis on hits or on uploaded sequences; PHYLIP-based analyses.
http://www.pathogenomics.bc.ca/phyloBLAST/

PHYLIP - (Found June 29, 2008 )

Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.
http://evolution.genetics.washington.edu/phylip.html

CIPRes - (Found June 29, 2008 )

The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and training initiatives. The website also contains a substantial list of links to related software.
http://www.phylo.org/

cpnDB - (Found June 29, 2008 )

cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.
http://cpndb.cbr.nrc.ca/home.php