IVisTMSA Version 2.0 (Interactive Visual Tools for Multiple Sequence Alignments Version 2.0) is visual tool in support of control, analysis, editing as well as annotation of several sequence association. The proposed version offers several analysis and editing features. Firstly, it shows sequence annotation in graphical form such as tooltips to show certain information, highlighting matches, mismatches, gaps and Highlight significant sequence place of residues phosphorylated/glycosylated. Secondly, it allows the user to lock sequences for synchronized hand alignment adjustments and prevent accidental edits. Thirdly, it also permits the user to calculate protein hydrophobicity / hydrophilicity plot. Fourthly, show chart view in sequences and alignment wise. Fifthly, it also allows the user to import of compatible formats directly from the clipboard without saving to a file first. Other features include downloading sequences from EMBL/GenBank/UniProt. IVisTMSA Version 2.0 has been developed using Java programing language and Netbeans IDE 8.0.