Tag: Multiple Alignment

MaM 1.4.2 – Manipulate Multiple Alignments of Genomic Sequences

MaM 1.4.2

:: DESCRIPTION

MaM (Multiple Alignment Manipulator) is a software tool that processes and manipulates multiple alignments of genomic sequences.MaM computes the exact locations of common repeat elements in multiple aligned sequences, provided by a variety of user identified programs databases and tables.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MaM

:: MORE INFORMATION

Citation

“Manipulating Multiple Sequence Alignments via MaM and WebMaM“,
Can Alkan, Eray Tuzun, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, S. Cenk Sahinalp.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W295-8.

BARCOD 1.0 – Multiple Alignment

BARCOD 1.0

:: DESCRIPTION

BARCOD encodes a multiple alignment according to the method developed by Véronique Barriel (C.R.Acad.Sci.III 317(7):693-701).From a an existing alignment (which will not be changed) BARCOD builds a character matrix suitable for use in phylogeny recontstruction programs. The method allows to encode each insertion/deletion event as one single event (whatever the number of nucleotides involved), while retaining any indel common to two or more taxa as a possibly shared character.

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsx/Linux
  • Java

:: DOWNLOAD

 BARCOD

:: MORE INFORMATION

MACSIMS 1.42 – Multiple Alignment of Complete Sequences Information Management System

MACSIMS 1.42

:: DESCRIPTION

MACSIMS (Multiple Alignment of Complete Sequences Information Management System) is a multiple alignment-based information management system that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is mined automatically from the public databases. In the MACS, homologous regions are identified and the mined data is evaluated and propagated from known to unknown sequences with these reliable regions. MACSIMS provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist.

::DEVELOPER

Julie Dawn Thompson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MACSIMS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jun 23;7:318.
MACSIMS: multiple alignment of complete sequences information management system.
Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, Plewniak F, Poch O.

Mview 1.67 – Multiple Alignment Viewer

Mview 1.67

:: DESCRIPTION

Mview is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed.

Mview Online

::DEVELOPER

European Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Mview

:: MORE INFORMATION

Citation:

Bioinformatics. 1998;14(4):380-1.
MView: a web-compatible database search or multiple alignment viewer.
Brown NP, Leroy C, Sander C.

MISHIMA 2.3.1 – Method for Inferring Sequence History In Terms of Multiple Alignment

MISHIMA 2.3.1

:: DESCRIPTION

MISHIMA is a program for multiple DNA sequence alignment. It takes input in FASTA format and outputs the alignment in MISHIMA or CLUSTALW format.

::DEVELOPER

Saitou lab, NIG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MISHIMA

:: MORE INFORMATION

Citation

MISHIMA–a new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data.
Kryukov K, Saitou N.
BMC Bioinformatics. 2010 Mar 18;11:142. doi: 10.1186/1471-2105-11-142.

Jalview 2.11.1.4 – Multiple Alignment Editor

Jalview 2.11.1.4

:: DESCRIPTION

Jalview is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Jalview

:: MORE INFORMATION

Citation:

Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
“Jalview Version 2 – a multiple sequence alignment editor and analysis workbench”
Bioinformatics 25 (9) 1189-1191

MARNA 100729 – Server for Multiple Alignment of RNAs

MARNA 100729

:: DESCRIPTION

MARNA (Multiple Alignment of RNAs) is a multiple alignment of RNAs taking into consideration both the primary sequence and the secondary structure. It is based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases. Additionally, MARNA predicts a consensus sequence as well as a consensus structure.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MARNA

:: MORE INFORMATION

Citation

Sven Siebert and Rolf Backofen,
“MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons“,
Bioinformatics 2005, Volume 21, Issue 16, 3352-3359

RevTrans 2.0 – Multiple Alignment of Coding DNA from Aligned Amino Acid Sequences

RevTrans 2.0

:: DESCRIPTION

RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Python

:: DOWNLOAD

  RevTrans

:: MORE INFORMATION

Citation:

Rasmus Wernersson and Anders Gorm Pedersen.
RevTrans – Constructing alignments of coding DNA from aligned amino acid sequences.
Nucl. Acids Res., 2003, 31(13), 3537-3539.

 

Belvu 20120403 – Multiple Alignments Viewer

Belvu 20120403

:: DESCRIPTION

Belvu is an X-windows viewer for multiple sequence alignments. One of the main advantages of Belvu is that it has an extensive set of modes to color the residues. There are several ways to color them by conservation and by residue type (user-configurable). Other useful features are fetching of the Swissprot (or PIR) entries by double clicking and easy tracking of the position in the alignment.

In addition, Belvu is a phylogenetic tool. It can be used to generate distance matrices between sequences under a selection of distance metrics. These can be saved and used subsequently in other applications. Belvu also implements certain distance-based tree reconstruction algorithms – including import of externally generated distance matrices – and bootstrap phylogenetic reconstruction. These functions are available both in the GUI (meaning Belvu may also be used as a tree viewer) or as command-line options, making the program a potential component in phylogenetic software pipelines.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

Belvu

:: MORE INFORMATION

Citation:

“Scoredist: A simple and robust protein sequence distance estimator”
Erik LL Sonnhammer and Volker Hollich
BMC Bioinformatics 6:108 (2005)

Indelign 2.0.4 – Probabilistically Annotating Indels in Multiple Alignments

Indelign 2.0.4

:: DESCRIPTION

Indelign is a program that uses a probabilistic evolutionary model to compute the most likely scenario of insertions and deletions consistent with an input multiple alignment. It is also capable of modifying the given alignment so as to obtain a better agreement with the evolutionary model.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Indelign

:: MORE INFORMATION

Citation:

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Jaebum Kim and Saurabh Sinha
Bioinformatics. 2007 Feb 1;23(3):289-97.

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