Community Analyzer is a GUI based Comparative Metagenomic Analysis platform that can be used to perform interactive 'on the fly' analysis of a given set of metagenomes on a PC/laptop with modest hardware configurations. The tool can not only help in grouping/clustering the metagenomes based on the taxonomic composition of their inherent microbial communities, but also in identifying microbial (or taxonomic) groups that show high positive/negative correlations in their abundance patterns (across the analyzed communities). Such insights can be used for inferring probable interaction patterns within microbial communities and for identifying the key players (or signature microbial groups) present in a given microbial community. Networks of symbiotically interacting microbes can also be identified and visualized. Moreover, users can also visualize the results of their comparative analysis using Principal Component Analysis (PCA) based graphical layouts, spring graphs, distance-based trees, bar charts, trend graphs and color coded tables. Using these functionalities, users can assess the relative contribution of each taxa in shaping the structure of the analyzed microbial communities (corresponding to each metagenomic data set), in addition to gaining insights into the probable interaction patterns between the constituent taxonomic groups. The intermediate analysis results can be easily exported as GML files, tables and images for later reference. Analysis instances can be saved as session files which can later be imported to carry out further analysis.