Abstract
BackgroundGenome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme.FindingsIn this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes.ConclusionColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.
Highlights
Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees
In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees
Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches
Summary
E.g., analyzing protein family evolution [1,2,3] or lateral gene transfers [4,5,6,7], typically generate large sets of phylogenic trees Visual inspection of these trees is often necessary, as automated algorithms are not yet sufficiently flexible and reliable [8,9]. BMC Research Notes 2009, 2:155 http://www.biomedcentral.com/1756-0500/2/155 files afterwards The advantage of such implementation is that the manual customization jobs are greatly facilitated in a semi-automatic way; the disadvantages are obvious: users have to learn yet some other languages ( both are as simple as plain English and easy to learn for those who had programming experiences) and it's still difficult to apply the same set of commands to multiple tree-files. Requirements: 5.8 or latter version of PERL program http:/ /www.perl.org and 1.4 or latter version of BioPerl module http://www.bioperl.org
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
