Base-By-Base – Genome Pairwise & Multiple Alignment Editor

Base-By-Base

:: DESCRIPTION

Base-By-Base is a whole genome pairwise and multiple alignment editor. The program highlights differences between pairs of alignments and allows the user to easily navigate large alignments of similar sequences. Although Base-By-Base was intended as an editor and viewer for alignments of highly similar sequences, it is also provides many of the functions of other generic alignment editors.

::DEVELOPER

Dr. Chris Upton, University of Victoria, Biochemistry and Microbiology

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Base-By-Base

:: MORE INFORMATION

Citation:

Brodie, R., A.J. Smith, R.L. Roper, V. Tcherepanov, and C. Upton. 2004.
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments, BMC Bioinformatics, 5, 96.

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0

:: DESCRIPTION

Kalign is a fast and accurate multiple sequence alignment software.

Kalignvu is an lightweight viewer for multiple sequence alignments and phylogenetic trees.

Mumsa is a program to assess the quality of multiple sequence alignments.

::DEVELOPER

Dr. Erik Sonnhammer

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

Kalign ; Kalignvu / Mumsa

:: MORE INFORMATION

Citation:

Kalign – an accurate and fast multiple sequence alignment algorithm.
Lassmann T. and Erik L.L. Sonnhammer (2005)
BMC Bioinformatics, 6:298

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Lassmann T. and Erik L.L. Sonnhammer (2006)
Nucleic Acids Research, 34:W596-W599

ClustalW / ClustalX 2.1 – Multiple Sequence Alignment

ClustalW / ClustalX 2.1

:: DESCRIPTION

Clustal W is a general purpose multiple alignment program for DNA or proteins.

Clustal X provides a window-based user interface to the ClustalW multiple alignment program.

EBI ClustalW Server

::DEVELOPER

Clustal is currently maintained at the Conway Institute UCD Dublin by Des Higgins, Fabian Sievers, David Dineen, and Andreas Wilm.

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Mac OsX/ Linux

:: DOWNLOAD

ClustalW / ClustalX ; Documentation

:: MORE INFORMATION

Citation:

“Clustal W and Clustal X version 2.0″, Larkin M., et al. Bioinformatics 2007 23(21):2947-2948

Mandala 1.1.1 – Generate Seed Designs for Seeded Alignment Algorithms

Mandala 1.1.1

:: DESCRIPTION

Mandala is a software to generate seed designs for seeded alignment algorithms. Mandala can be used to improve the sensitivity of alignment in practice.

Mandala can design near-optimal seeds for similarity models derived empirically from a collection of biosequences.

::DEVELOPER

Jeremy Buhler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

Mandala Sourc Code (C++)

:: MORE INFORMATION

Citation

J. Buhler, U. Keich, and Y. Sun. “Designing Seeds for Similarity Search in Genomic DNA.” In Proceedings of the Seventh Annual Internation Conference on Computational Molecular Biology, Berlin, Germany, 67-75, 2003.