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Evol Bioinform Online. 2015 Mar 12;11:35-42. doi: 10.4137/EBO.S18980. eCollection 2015.

IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

Author information

1
Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
2
Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan.
3
Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
4
Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan. ; Department of Computer Science, NFC Institute of Engineering and Technology, Multan, Pakistan.
5
Institute for Web Science and Technologies, University of Koblenz-Landau, Germany.
6
Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan.
7
Department of Computer Science, The Islamia University of Bahawalpur, Pakistan.
8
Department of Physics, Government Sadiq Egerton College Bahawalpur (S.E. College Bahawalpur), Pakistan.

Abstract

IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix.

KEYWORDS:

FASTA; MSA Identity Matrix; MSA comparator; MSA editing tool

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