Phylemon 2.0: New resources in a suite of web tools for molecular evolution, phylogenetics and phylogenomics

TARRAGA J., MEDINA I., HUERTA-CEPAS J., ARBIZA L., SERRA F., GABALDÓN T., DOPAZO J. & H. DOPAZO

Barcelona. Spain

Congreso; Annual Meeting of the Society of Molecular Biology and Evoltion; 2008

Society for molecular biology and evolution

Phylemon 2.0: New resources in a suite of web tools for molecular evolution, phylogenetics and phylogenomics Tarraga J, Medina I, Huerta­Cepas J, Serra F, Arbiza L, Gabaldón T, Dopazo J and H Dopazo Bioinformatics Department. Centro de Investigación Príncipe Felipe Valencia. Spain Phylemon (http://phylemon.bioinfo.cipf.es/) is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular standalone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add molecular evolutionary and phylogenetic insight to their research. Tools included in Phylemon cover a wide yet selected range of programs; from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. New developments and improvements of this version are: 1­ The addition of a file, project, and job management package allowing users to move, rename, and delete files in their account, run jobs asynchronously, and download any or all of their data as compressed archives; 2­ A new version of the Enviorment for Tree Exploration (ETE) program, allowing interactive tree image manipulation for clearer images and ease of interpretaion; 3­ the addition of Lagan and Multi­Lagan programs wich are particularly usefull for the accurate alignment of long pairwise or multiple genomic sequences at large evolutionary distances, respectively; 4­ the addition of PHYML in the super­phylemon pipliner framework, introducing the possibility of searching for ML trees using the complete range of DNA or protein models of the program in a single click; 5­ the addition of the evolver program from PAML 4.0. which allows for simulations of nucleotide, codon, or amino acid sequence data; and finally, 6­ we added the PhylemonDB a database of multiple alignment and trees derived from phylogenomics projects like the Human Phylome Projects among others. This combination of improvements and additions in the Phylemon web server lead it to being the most complete and easy to use set of tools available on the web for the evolutionary and phylogenetic analysis of sequences.