MAFFT 7.450 – Multiple Alignment Program

MAFFT 7.450

:: DESCRIPTION

MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc.

MAFFT Server

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux

:: DOWNLOAD

MAFFT

:: MORE INFORMATION

Citation

Katoh, Rozewicki, Yamada 2019
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Briefings in Bioinformatics 20:1160-1166

Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees.
Yamada KD, Tomii K, Katoh K.
Bioinformatics. 2016 Jul 4. pii: btw412

Kazutaka Katoh and Hiroyuki Toh
Parallelization of the MAFFT multiple sequence alignment program
Bioinformatics (2010) 26 (15): 1899-1900

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.

Jalview 2.11.0 – Multiple Alignment Editor

Jalview 2.11.0

:: 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

Gblocks 0.91b – Selection of Conserved Blocks from multiple alignments for their use in Phylogenetic Snalysis

Gblocks 0.91b

:: DESCRIPTION

Gblocks is a computer program written in C that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

  Gblocks

:: MORE INFORMATION

Citation:

Talavera, G., and Castresana, J. (2007).
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Systematic Biology 56, 564-577.

Facet v1.4 – Multiple Alignment Accuracy Estimation and Parameter Advising

Facet v1.4

:: DESCRIPTION

Facet (Feature-based accuracy estimator) computes a single estimate of accuracy as a linear combination of efficiently-computable feature functions.

::DEVELOPER

Dr. Dan DeBlasio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs

:: DOWNLOAD

Facet

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Apr;20(4):259-79. doi: 10.1089/cmb.2013.0007. Epub 2013 Mar 14.
Accuracy estimation and parameter advising for protein multiple sequence alignment.
Kececioglu J, DeBlasio D.

Magma 1.0 – Multiple Aligner of Genomic Multiple Alignments

Magma 1.0

:: DESCRIPTION

Magma is a fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 Magma

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Feb;19(2):139-47. doi: 10.1089/cmb.2011.0249.
Fast, sensitive discovery of conserved genome-wide motifs.
Ihuegbu NE, Stormo GD, Buhler J.

BetaTPred2: Prediction of Beta-turns in Proteins using Neural Networks and Multiple Alignment

BetaTPred2

:: DESCRIPTION

The aim of BetaTPred2 server is to predict Beta turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ? turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED. The net is trained and tested on a set of 426 non-homologous protein chains with 7-fold cross-validation. It predicts ? turns in proteins with residue accuracy of 75.5% and MCC value of 0.43.

::DEVELOPER

BetaTPred2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S.
Prediction of beta-turns in proteins from multiple alignment using neural network.
Protein Science 2003 12: 627-634