MolPhase is an advanced algorithm designed to predict protein phase separation (PS) behavior, enhancing accuracy and reliability by incorporating diverse physicochemical features and extensive experimental datasets. The algorithm applies a user-friendly interface to compare biophysical features alongside protein sequences, facilitating the identification of new phase-separating proteins and guiding hypothesis generation and experimental design. Key contributing factors include electrostatic pi-interactions, disorder, and prion-like domains. MolPhase's performance is validated through the study of phytobacterial type III effectors (T3Es), which are found to be highly prone to homotypic PS, a finding experimentally validated in vitro and in vivo. The algorithm's effectiveness is demonstrated by its ability to accurately predict PS behavior in various conditions, outperforming other phase separation predictors. MolPhase's online interface provides a comprehensive tool for researchers to predict and analyze phase separation in biological systems, aiding in hypothesis formulation and experimental design.MolPhase is an advanced algorithm designed to predict protein phase separation (PS) behavior, enhancing accuracy and reliability by incorporating diverse physicochemical features and extensive experimental datasets. The algorithm applies a user-friendly interface to compare biophysical features alongside protein sequences, facilitating the identification of new phase-separating proteins and guiding hypothesis generation and experimental design. Key contributing factors include electrostatic pi-interactions, disorder, and prion-like domains. MolPhase's performance is validated through the study of phytobacterial type III effectors (T3Es), which are found to be highly prone to homotypic PS, a finding experimentally validated in vitro and in vivo. The algorithm's effectiveness is demonstrated by its ability to accurately predict PS behavior in various conditions, outperforming other phase separation predictors. MolPhase's online interface provides a comprehensive tool for researchers to predict and analyze phase separation in biological systems, aiding in hypothesis formulation and experimental design.