ALVIS 0.1 – Explorative Analysis and Visualisation of Multiple Sequence Alignments

ALVIS 0.1

:: DESCRIPTION

Alvis (Interactive non-aggregative multiple sequence ALignment VISualisation) is an open-source platform for the joint explorative analysis of MSAs and phylogenetic trees, employing Sequence Bundles as its main visualisation method.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

ALVIS

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2016 May 5;44(8):e77. doi: 10.1093/nar/gkw022.
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N.

msa 1.18.0 – An R Package for Multiple Sequence Alignment

msa 1.18.0

:: DESCRIPTION

msa provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 msa

:: MORE INFORMATION

Citation

msa: an R package for multiple sequence alignment.
Bodenhofer U, Bonatesta E, Horejš-Kainrath C, Hochreiter S.
Bioinformatics. 2015 Aug 26. pii: btv494.

TreeLign / FastTreeLign – Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics

TreeLign / FastTreeLign

:: DESCRIPTION

TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Perl

:: DOWNLOAD

 TreeLign

:: MORE INFORMATION

FitchAln 20100321 – Given Phylogenetic Tree and Multiple Sequence Alignment, show the Fitch Score Matrix

FitchAln 20100321

:: DESCRIPTION

Given a newick binary tree T and its correpsonding multiple sequence alignemnt A of size n x m, where n is the number of leaf nodes in T and m is the length of the alignment, FitchAln generates a (n-1) x (m+1) Fitch score matrix representing the (Maximum Parsimony) number of mutations for each site for each internal node.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 FitchAln

:: MORE INFORMATION

AlignmentComparator 1.1.0 – Visualize and Annotate Differences between Alternative Multiple Sequence Alignments

AlignmentComparator 1.1.0

:: DESCRIPTION

AlignmentComparator is a GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same data set.

::DEVELOPER

BioInfWeb projects,

:: SCREENSHOTS

AlignmentComparator

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

 AlignmentComparator

:: MORE INFORMATION

Citation

Stöver BC, Müller KF:
AlignmentComparator – A GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments.
4th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2014

LibrAlign 0.9.0 – Displaying and Editing Multiple Sequence Alignments and Attached Data

LibrAlign 0.9.0

:: DESCRIPTION

LibrAlign is a Java library for creating graphical user interfaces dealing with multiple sequence alignments and attached raw and meta data. It is is fully interoperable with the BioJava 3 API and all components are provided in a native Swing and a native SWT version.

::DEVELOPER

BioInfWeb projects

:: SCREENSHOTS

LibrAlign

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Java

 LibrAlign

:: MORE INFORMATION

Citation

Stöver BC, Müller KF
LibrAlign – A Java library with powerful GUI components for multiple sequence alignment and attached raw and meta data
German Conference on Bioinformatics (GCB); Bielefeld, Germany; 2014

OXBench 1.3 – Evaluate Accuracy of Protein Multiple Sequence Alignment

OXBench 1.3

:: DESCRIPTION

OXBench includes data and software to evaluate the accuracy of protein multiple sequence alignments.  It is a benchmark suite for multiple alignment algorithms that includes a large set of test alignments and software to aid in analysis of a method’s performance or relative performance.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

OXBench

:: MORE INFORMATION

Citation:

Raghava, G. P. S., Searle, S. M. J., Audley, P. C, Barber, J. D. and Barton, G. J.
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy
(2003), BMC Bioinformatics, 4:47

T-Coffee 13.39.0 – Multiple Sequence Alignment Tools

T-Coffee 13.39.0

:: DESCRIPTION

T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle…) into one unique alignment.

T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee).

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows with Cygwin/Mac OsX/ Linux

:: DOWNLOAD

T-Coffee

:: MORE INFORMATION

Citation:

T-Coffee: A novel method for multiple sequence alignments.
Notredame,Higgins,Heringa,JMB,302(205-217)2000[medline]

M-Coffee – Combination of Multiple Sequence Alignment Packages

M-Coffee

:: DESCRIPTION

M-Coffee is a multiple sequence alignment Package. It is part of the T-Coffee distribution. The specificity of M-Coffee is that rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignents into one unique final alignment.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

M-Coffee: combining multiple sequence alignment methods with T-Coffee.
Wallace IM, O’Sullivan O, Higgins DG, Notredame C.
Nucleic Acids Res. 2006 Mar 23;34(6):1692-9. Print 2006.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.

TCS – Evaluation and Filtering of multiple Sequence Alignments

TCS

:: DESCRIPTION

TCS (Transitive Consistency Score) web server is a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.
Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.
Nucleic Acids Res. 2015 Apr 8. pii: gkv310.