Taxonomic colouring of phylogenetic trees of protein sequences.
BACKGROUND
Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common.


RESULTS
We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree.


CONCLUSIONS
PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.
Palidwor
Gareth
G
Ontario Genomics Innovation Centre, Ottawa Health Research Institute, 501 Smyth, Ottawa, ON K1H 8L6, Canada. gpalidwor@ohri.ca
Reynaud
Emmanuel G
EG
Andrade-Navarro
Miguel A
MA
D000465:Algorithms; D000595:Amino Acid Sequence; D003116:Color; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D020543:Proteome / Q000145:classification* / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D020543:Proteome