IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

Developer: M.T.Pervez

Virtual University of Pakistan





IVisTMSA is a software package of seven interactive visual tools for multiple sequence alignments. Major focus is on manipulating large alignments.

MSApad is an editing and analysis tool for multiple sequence alignments. It can load 409% big alignments than Jalview, STRAP, CINEMA and Base by Base. It has implemented divide and conquer approach for efficient computation of consensus and conserved sequence, distance matrix for phylogenetic tree and identity of sequences. It also has several unique editing features.

MSA comparator (MQAT version 2.0.1) provides a new feature that allows the user to evaluate where the reference and test alignments have conserved regions.

MSA reconstruction tool provides graphical user interfaces for Clustal Omega, ClustalW2, MAFFT, MUSCLE and BioJava implementation of the algorithm of Smith and Waterman.  MSA reconstruction provides feature to load several sequences files simultaneously.

FASTA generator converts alignments of ClustalW, MSF, Phylip, PIR, GDE and Nexus formats of unlimited size into FASTA format.

MSA ID calculator is a tool to calculate identity matrix of two MSAs efficiently. It calculated identity matrix of two alignments having 8070 sequences and 2696 base pairs just in 12 minutes.

Tree calculation tool generates a phylogenetic tree using neighbor joining % identity and BLOSUM 62 matrix and provides

Distance Matrix calculating tool generates distance matrix using neighbor joining % identity and BLOSUM62 for smaller alignments efficiently.


Download IVisTMSA

Download MQAT

Download E-SICT

Download test files for comparative study of MSA methods

Obselete versions offer only a subset of the functionalities of the distribution version. When testing new alignment comparison tools, please compare against only the newest version of MQAT!

Version 1.0.1
Version 1.0


Muhammad Tariq Pervez,Masroor Ellahi Babar,Asif Nadeem,Naeem Aslam,Sarfraz Ahmad,Shah Muhammad,Salman Qadri,Muhammad shahid,Tanveer Hussain,Maryam Javed. IVistMSA: Interactive Visual Tools for Multiple Sequence Alignments. Evolutionary Bioinformatics (In Process).

Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Muhammad Aslam, Ali Raza Awan, Naeem Aslam, Tanveer Hussain, Nasir Naveed, Salman Qadri, Usman Waheed and Muhammad Shoaib. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods. Evolutinary Bioinformatics 2014: 10 1-13.

M.T.Pervez, N.Aslam, S.Muhammad, S.Qadri, S.Awan. 2014. A Methodology To Enhance Programming Skills Of E-Learning Students. Pakistan Journal of Science.  Local, Higher Education Commission (HEC) of Pakistan recognized journal.

Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Naeem Aslam, Ali Raza, Muhammad Aslam, Tanveer Hussain, Salman Qadri, Sarfraz Ahmad and Muhammad Shoaib. MQAT: An Efficient Quality Assessment Tool for Large Multiple Sequence Alignments. Life Sci J 2013;10(9s):9-16

Muhammad Tariq Pervez Naeem Aslam, Sarfraz Ahmad, Syed Shah Muhammad, Salman Qadri, Sajid Ali andUsman Waheed. FAQMAA: A Framework for Automatic Quality Assessment of Multiple Sequence Alignments. Life Sci J 2013;10(9s):41-45.

Tariq, M.P., Shoaib, M., S. Arshad ,. and S.Qadri. 2011. Filtering VIP Emails Using Dynamic Weight Assignment Technique. Pakistan Journal of Science. Local, Higher Education Commission (HEC) of Pakistan recognized journal.

Tariq, M.P., M. Aslam, S. Ahmed, M. Faisal and S. Ubaid. 2010. EMMCGID: A Methodology for E-Learning Universities. Pakistan Journal of Science.

Tariq, M.P., Waqar M. Mirza and Akbar R. Multi-agent Based University Time Table Scheduling System (MUTSS). International Journal of Multidisciplinary Sciences and Engineering, 1(1), 2010

Tariq, M.P., T.Mehmood, M.F.Shahzad, M. Nasir. 2010. Open Source Software in E-Learning Environment: Observations and Experiences. Fourth International Conference on Open-Source Systems and Technologies 22-24 December 2010, Lahore, Pakistan, 27-33. ,

Tariq, M.P., M.F. Shahzad, M. Tahir, M. Nasir. 2010. Algorithm: A Back Bone of Bio-Informatics. Bioinformatics – Opening Up New Frontiers in Molecular Biology Research, 14-15, 2010, 27-33. ,

Aslam, M., M.P.Tariq, S. Muhammad S. Mushtaq and A. M. M. Enriquez. 2010. FMSIND: A Framework of Multi-agent Systems Interaction during Natural Disaster.Journal of American Science, 6(5). 217-224. ,

Qadri, S., M.P.Tariq and M. Shoaib. 2010. A Comparative Study of Semantic Cache Techniques in Mobile Database Environment. Pakistan Journal of Science. 62(1).55-59 ,

Aslam, M., A. M. M. Enriquez, M.P.Tariq and Z. Saeed. 2010. An Expertise Recommender System for Web Cooperative Production. Journal of American Science, 6(7).106-112. ,

Tayybah K., Shoaib M., Tariq M.P., Sonia M., Qazi and Mudassar I. 2010. An Approach to Partially Import the Ontologies on Semantic Web Based Upon User Choice. Journal of American Science, 6(11).571-581. Year: November, 2010 ,

Ali, A., S. Qadri, S. S. Muhammad , J. Abbas, M. P. Tariq and S. Awan. 2010. Software Cost Estimation through Entity Relationship Model Journal of American Science, 6(11).47-51. ,

Shoaib, M., S. Arshad, S. Jabeen and M.P.Tariq. 2010. Software quality metrics for Rhetorical Structure Theory based Information Retrieval Systems. 2010. Pakistan Journal of Science. ,

Version History

MQAT version 1.0.2(April. 04, 2013)

Feature Addition: Added featrue of saving the whole work in form of a project/p>

Feature Addition: Added featrue of printing all or selected data/charts

Feature Addition: Added featrue of convertring data into HTML and PDF format

MQAT version 1.0.1(January. 22, 2013)

Feature Addition: Added featrue of graphical analaysis of test alignmetns via bar, pie and line charts

Feature Addition: Added featrue of editing of varous parameters of graphical tools of analysis of test alignments

Bug fix: Fixed Out-of-bounds exception for test alignments.

MQAT version 1.0(Nov. 15, 2012)

Designed and implemented multithreaded algorithm

Text format view in tabular form

Added sorting features (ascedning and descending)