Previously we developed the stand-alone SNAP Workbench toolkit that integrated a wide array of bioinformatics tools for phylogenetic and population genetic analyses. We have now developed a web-based portal front-end, using the Mobyle portal framework, which executes all of the programs available in the stand-alone SNAP Workbench toolkit on a high-performance Linux cluster. Additionally, we have expanded the selection of programs to over 189 tools, including population genetic, genome assembly and analysis tools, as well as metagenomic and large-scale phylogenetic analyses. The Mobyle SNAP Workbench web portal allows end users to (i) execute and manage otherwise complex command-line programs, (ii) launch multiple exploratory analyses of parameter-rich and computationally intensive methods and (iii) track the sequence of steps and parameters that were used to perform a specific analysis. Analysis pipelines or workflows for population genetic, metagenomic and genome assembly provide automation of data conversion, analysis and graphical visualization for biological inference.