Soft polytomies emerge due to the application of handmade supertrees in phylogenetic community analysis, thus increasing uncertainties regarding phylogenetic diversity or community structure indices. Real-time integration of advances in phylogenetic knowledge among species from public data repositories, such as Open Tree of Life, may reduce this uncertainty. Based on an interface with Open Tree of Life, the Community Tree Optimizer (ComTreeOpt) classifies families from user-specific lists into resolvable and non-resolvable families, builds resolved subtrees for resolvable families and inserts them in the megatree previously pruned to species from non-resolvable families. Community trees optimized by ComTreeOpt show 30–50% fewer polytomies than non-optimized community trees, reducing the uncertainties in phylogenetic diversity and dispersion metrics that are due to a lack of phylogenetic resolution. ComTreeOpt enhances user-specific community trees in a rapid and inexpensive way based on available phylogenetic information, thus increasing the confidence in the metrics of phylogenetic diversity and dispersion.