PHY.FI: fast and easy online creation and manipulation of phylogeny color figures

BMC Bioinformatics. 2006 Jun 22;7:315. doi: 10.1186/1471-2105-7-315.

Abstract

Background: The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too.

Results: This paper presents an online tool, PHY.FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY.FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format.

Conclusion: PHY.FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY.FI is free for all and is available from this web address: http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Color*
  • Computer Graphics*
  • Models, Genetic*
  • Online Systems
  • Phylogeny*
  • Software*
  • User-Computer Interface*