Tag: Multiple Sequence Alignment

xalign 6.1 – Multiple Sequence Alignment

xalign 6.1

:: DESCRIPTION

xalign is a tool for multiple sequence alignment based on sequence homology and secondary structure. The user has the ability to include specific insights or knowledge into the alignment through sequence anchoring, clustering, changing the amino acid similarity matrix, gapping penalties, or even the order in which the sequences are aligned.

::DEVELOPER

Brian Sykes Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 xalign

:: MORE INFORMATION

Citation

David Wishart, Robert Boyko, Tim Jellard, Brian Sykes
Constrained multiple sequence alignment using XALIGN
Cabios Vol. 10 no.6 1994 Pages 687-688

RNAstrand 2.0.0 – Predict Reading Direction of Structured RNAs in Multiple Sequence Alignments

RNAstrand 2.0.0

:: DESCRIPTION

RNAstrand predicts the reading direction of a structured RNA gene from a multiple sequence alignment and its reverse complement. It is meant as a post processing tool for RNA prediction tools which in general do not reliable annotate the reading direction of the structured RNA candidate.

RNAstrand Online Version

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RNAstrand

:: MORE INFORMATION

Citation

RNAstrand: Reading direction of structured RNAs in multiple sequence alignments
Kristin Reiche, Peter F. Stadler,
Algorithms for Molecular Biology, 2:6, 2007.

noisy 1.5.12 – Identify Homo-plastic Characters in Multiple Sequence Alignments

noisy 1.5.12

:: DESCRIPTION

Noisy is a software to identify homo-plastic characters in multiple sequence alignments.In a first phase the rows of the input multiple sequence alignment (MSA) in multi fasta format are reordered to conform to a circular ordering. For this purpose noisy includes the corresponding subset of routines from David Bryant and Vincent Moulton’s NeighborNet and Stefan Grünewald’s QNet packages. Subsequently, a reliability score for each column of the reordered MSA is calculated. Essentially, the number of character state alterations in an alignment column is counted and compared to the observed count in random shufflings of the column. The uniform pseudo-random number generator Mersenne Twister is used to generate the random shufflings of alignment columns.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 noisy

:: MORE INFORMATION

Citation

Andreas W. M.Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
Noisy: identification of problematic columns in multiple sequence alignments.
Algorithms Mol Biol, 3:7 (2008).

Gmaj 20081103 – Interactive Viewer for Multiple Sequence Alignments

Gmaj 20081103

:: DESCRIPTION

Gmaj is a tool designed for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by sequence-symmetric alignment programs such as TBA (though it can also be used with MAF format alignments from other sources). It can display interactive graphical and text representations of the alignments, diagrams showing the locations of exons and repeats, and other annotations — all with the user’s choice of reference sequence.

::DEVELOPER

Miller Lab at Penn State University Center for Comparative Genomics and Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Gmaj

:: MORE INFORMATION

Anchored DIALIGN 2.2.2 – Multiple Sequence Alignment with User-defined Constraints

Anchored DIALIGN 2.2.2

:: DESCRIPTION

Anchored DIALIGN is a WWW server for multiple alignment of protein and nucleic acid sequences using DIALIGN with user-defined anchor points.Alignments can be created either fully automatically or by using a list of user-defined constraints. By specifying such anchor points, the user can force the program to align selected segments of the sequences to each other. The remaining parts of the sequences are then aligned automatically, respecting the constraints imposed by the selected anchor points.

Anchored DIALIGN Online Version

::DEVELOPER

Burkhard Morgenstern et al.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Anchored DIALIGN

:: MORE INFORMATION

Citation

B. Morgenstern, S.J. Prohaska, D. P?hler, P.F. Stadler (2006)
Multiple sequence alignment with user-defined anchor points
Algorithms for Molecular Biology 1,6.

MUSCLE 3.8.31 – Multiple Sequence Alignment

MUSCLE 3.8.31

:: DESCRIPTION

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that gave the best average benchmark accuracy in my tests. However, benchmark accuracy is a rather dubious measure

MUSCLE Online version

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

MUSCLE

:: MORE INFORMATION

Citation

Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.

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