Current frameworks of side-by-side phylogenetic trees comparison face two issues: (1) accepting mainly binary trees as input and (2) assuming input trees having identical or highly overlapping taxa. However, cladistic comparative studies often lead with multiple nontotally resolved trees with nonidentical sets of taxa. We tackle these issues in this study, presenting the iPhyloC, an interactive web-based framework for comparing phylogenetic trees side by side. iPhyloC supports automatic identification of the common taxa in the input trees, comparison options between them, intuitive design, high usability, scalability to large trees, and cross-platform support. iPhyloC was tested using different trees and a supertree depicting the phylogenetic relationships within the insect order Diptera as examples.