PHYLOVIEWER

Abstract

As the number of sequenced genomes rapidly increases, opportunities for testing phylogenetic hypotheses at the genome-wide level continue to increase. To support the presentation and manipulation of phylogenetic trees with diverse information, a web-based tree viewer, named Phyloviewer (http://phyloviewer.riceblast.snu.ac.kr), was developed based on Bioinformatic Portal System (BPS; http://bps.bio-os.net/intro.php). The Phyloviewer consists of two parts: Tree Parser analyzes tree files and Tree Viewer displays phylogenetic tree as a graphic file on a web browser. The Tree Parser can analyze data in the phb file format, and additional formats will be supported in the future. On the web interface, users can manipulate phylogenetic trees, such as collapsing certain branches of the tree at specific internal nodes and tagging comments on a node. In addition, the information content of the tree can be enriched by adding extended information of the sequences used, such as the InterPro domain architecture stored in an annotation database of the Comparative Fungal Genomic Platform (CFGP; http://cfgp.snu.ac.kr). The Phyloviewer has already been implemented in several bioinformatics systems to generate phylogenetic trees and provide interactive interface for manipulating the trees.


You can download the poster of Phyloviewer here.

Introduction

Phylogenetic analyses has an important role to determine the functions of uncharacterized genes by evolutionary analysis with sequence dataset from different species.(Eisen, 1998). Nowadays, increasing number of genome sequencing give us more opportunities for testing phylogenetic hypotheses at the genome-wide level by using archived database.

 Phylogenetic pipeline generation has been developed by several research groups with providing the integrated tools. Phylemon (Joaqu©¥¢¥n Ta¢¥ rraga, 2007) contains useful tools such as ClustalW (Julie D. Thompson, 1994) and Muscle (Edgar, 2004) for the sequence alignment. It also provides phylogeny analysis and evolutionary tools. PhyloBuilder (Jake Gunn Glanville, 2007) web server provides an integrated phylogenomic pipeline starting from the submitted sequence to many useful functions such as homolog identification, multiple sequence alignment, phylogenetic tree drawing tool, subfamily identification and structure prediction.

 Researchers need to manipulate phylogenetic trees because well presented trees are required to explain the hypotheses clearly, and the related researches were already conducted. MEGA 4.0(Koichiro Tamura, 2007) is widely used program for generating and manipulating phylogenetic tree on the local computer. Web-based tools such as PHY-FI (Fredslund, 2006) allow users to change the size, font, and color of the tree on the web browser. PhyloView (Gareth Palidwor, 2006) has been made for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree.

 TreeDomViewer (Blaise T. F. Alako, 2006) is a visualization tool combining phylogenetic tree description, multiple sequence alignment and InterProScan data of sequences. It also generates a phylogenetic tree projecting the corresponding protein domain information onto the multiple sequence alignment. PhyloFacts(Nandini Krishnamurthy, 2006) have been developed for protein functional and structural classification as an online structural phylogenomic encyclopedia, and it provides many informative data such as InterPro, GO term, and EC Number.

 To support the presentation and manipulation of phylogenetic trees with diverse information in the different kinds of web-based database, the component of the system named Phyloviewer (http://www.phyloviewer.org), was developed based on Bioinformatic Portal System (BPS; http://bps.bio-os.net/intro.php). The Phyloviewer has already been implemented in several bioinformatics systems to generate phylogenetic trees and provide interactive interface for manipulating the trees. FTFD (Park, et al. Unpublished), CFGP (Jongsun Park, In Press), Phytophthora Database (Park, et al, Unpublished), and IMGD (Lee, et al. Unpublished) are the examples already have been made.