PSAR / PSAR-Align – Measuring Multiple Sequence Alignment Reliability by Probabilistic Sampling

PSAR / PSAR-Align

:: DESCRIPTION

PSAR (probabilistic sampling-based alignment reliability) is a software to the alignments in the UCSC Genome Browser to measure the reliability of alignments in different types of regions, such as coding exons and conserved non-coding regions, and use it to guide cross-species conservation study.

PSAR-Align is a software of improving multiple sequence alignment using probabilistic sampling

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

PSAR ; PSAR-Align

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 1;30(7):1010-2. doi: 10.1093/bioinformatics/btt636. Epub 2013 Nov 12.
PSAR-align: improving multiple sequence alignment using probabilistic sampling.
Kim J1, Ma J.

Nucleic Acids Res. 2011 Aug;39(15):6359-68. Epub 2011 May 16.
PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.
Kim J, Ma J.

Clustal Omega 1.2.4 – Multiple Sequence Alignment

Clustal Omega 1.2.4

:: DESCRIPTION

Clustal Omega is a multiple sequence alignment program for proteins. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

Clustal Omega Online Version

::DEVELOPER

the Conway Institute UCD Dublinby Des Higgins, Fabian Sievers, David Dineen, and Andreas Wilm.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Clustal Omega

:: MORE INFORMATION

Citation:

Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, S?ding J, Thompson JD, Higgins DG (2011)
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Molecular Systems Biology 7 Article number: 539 doi:10.1038/msb.2011.75

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]