Taxonomic colouring of phylogenetic trees of protein sequences

BMC Bioinformatics
Gareth PalidworMiguel A Andrade-Navarro

Abstract

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. 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 ta...Continue Reading

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Citations

Jun 6, 2009·Nature Reviews. Neurology·Chiara Zuccato, Elena Cattaneo
Feb 4, 2010·PloS One·Ralph PethicaJulian Gough
Jan 19, 2012·Evolutionary Bioinformatics Online·Sylvain Lespinats, Bernard Fertil
Jan 6, 2016·Applied and Environmental Microbiology·Jennifer L Seffernick, Lawrence P Wackett

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Methods Mentioned

BETA
GTPases

Software Mentioned

Adobe SVG viewer
BioPerl
MacClade
PhyloView
SVG
Internet Explorer
Mesquite
SpTrembl
Perl RecDescent
MacOS

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