![]() ![]() Here, we outline the main characteristics of the server and the new developments added to this version. The main objective of Phylemon is to provide to expert and non-expert users all necessary applications in a single integrated web framework that guides them through the whole sequence evolutionary analysis. Phylemon 2.0 has several unique features that differentiates it from other resources: (i) it offers an integrated environment that enables the concatenation of evolutionary analyses, the storage of results and that handles format conversions transparently (ii) once an output file is produced, Phylemon suggests other possible analyses that could logically follow, thus guiding the user through the web server and finally (iii) users can build and save complete pipelines to be automatically used on many genes in subsequent sessions (phylogenomics). Phylemon 2.0 covers a wide, yet selected, range of programs, integrating over 30 different tools for phylogenetic and evolutionary analyses. Phylemon was originally developed in 2007 as a web server providing a common framework to run the most frequent analyses on DNA and protein sequences from a phylogenetic and evolutionary perspective. see ), ( ) ( 5 ), CIPRES ( ) and Phylemon ( 6 ) developed the concept of integrated platforms, which implement different phylogenetic analysis programs in a single server. ![]() In the second category, resources such as the ‘Pasteur server’ (e.g. Among the first are servers that execute multiple sequence alignment (MSA) tools such as ClustalW ( 3 ) ( ), or sophisticated programs to test molecular adaptation such as the HyPhy environment ( 4 ) ( ). Web servers for phylogenetic and evolutionary analyses range from those running single programs to those integrating multiple tools. Phylogenetic analysis and model-based hypothesis testing are essential elements in current molecular evolution studies ( 1, 2 ). ![]()
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