title: IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.
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.
authors: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors: Muhammad Tariq
authors: MT
authors: Pervez
authors: Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan.
authors: Masroor Ellahi
authors: ME
authors: Babar
authors: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors: Asif
authors: A
authors: Nadeem
authors: 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.
authors: Naeem
authors: N
authors: Aslam
authors: Institute for Web Science and Technologies, University of Koblenz-Landau, Germany.
authors: Nasir
authors: N
authors: Naveed
authors: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan.
authors: Sarfraz
authors: S
authors: Ahmad
authors: Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan.
authors: Shah
authors: S
authors: Muhammad
authors: Department of Computer Science, The Islamia University of Bahawalpur, Pakistan.
authors: Salman
authors: S
authors: Qadri
authors: Department of Physics, Government Sadiq Egerton College Bahawalpur (S.E. College Bahawalpur), Pakistan.
authors: Muhammad
authors: M
authors: Shahid
authors: Department of Bioinformatics, Virtual University of Pakistan, Lahore, Pakistan.
authors: Tanveer
authors: T
authors: Hussain
authors: Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan.
authors: Maryam
authors: M
authors: Javed
keywords: FASTA; MSA Identity Matrix; MSA comparator; MSA editing tool