Tag: Multiple Sequence Alignment

OMA 0.98 – Optimal Multiple Sequence Alignment

OMA 0.98

:: DESCRIPTION

OMA (Optimal Multiple Sequence Alignment) is a library of C++-classes for the optimal alignment of sequences, built upon the Library of Efficient Data structures and Algorithms (LEDA). The parts of the library build a hierarchical, modular system, so that one can rearrange blocks or replace predefined modules by ones own classes.

::DEVELOPER

Torsten Will, Knut Reinert, Jens Stoye

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / solaris

:: DOWNLOAD

OMA

:: MORE INFORMATION

Citation

Knut Reinert,Jens Stoye,Torsten Will:
The extended abstract Combining Divide-and-Conquer, the A*-Algorithm and Successive Realignment Approach to Speed up Multiple Sequence, (GCB 99).

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

AQUA 1.1 – Automatic Quality Improvment for Multiple Sequence Alignment

AQUA 1.1

:: DESCRIPTION

AQUA (Automated quality improvement for multiple sequence alignments)is a s implementation which relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD)

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AQUA

:: MORE INFORMATION

Citation

Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P.
AQUA: automated quality improvement for multiple sequence alignments.
Bioinformatics. 2010 Jan 15;26(2):263-5. Epub 2009 Nov 19.

DCA 1.1 – Divide-and-Conquer Multiple Sequence Alignment

DCA 1.1

:: DESCRIPTION

DCA (Divide-and-Conquer Multiple Sequence Alignment) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences. The program is based on the DCA algorithm, a heuristic approach to sum-of-pairs (SP) optimal alignment that has been developed at the FSPM over the years 1995-97.

::DEVELOPER

Jens Stoye

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DCA

:: MORE INFORMATION

Citation

Divide-and-Conquer Multiple Sequence Alignment
J. Stoye
Dissertation Thesis. Universität Bielefeld, Forschungsbericht der Technischen Fakultät, Abteilung Informationstechnik, Report 97-02, 1997. (ISSN 0946-7831)

Dialign 2.2.1 / DIALIGN-TX 1.0.2 – Multiple Sequence Alignments

Dialign 2.2.1 / DIALIGN-TX 1.0.2

:: DESCRIPTION

DIALIGN is a novel alignment program based on segment-to-segment comparison.It is especially suited to detect local similarities among distantly related sequences.DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.

DIALIGN-TX is a substantial improvement of DIALIGN-T that combines greedy and progressive alignment strategies in a new algorithm. DIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greedy approach to assemble multiple alignments from local pairwise sequence similarities. Such greedy approaches may be vulnerable to spurious random similarities and can therefore lead to suboptimal results.

::DEVELOPER

Burkhard Morgenstern et al.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Dialign ; DIALIGN-TX

:: MORE INFORMATION

Citation

B. Morgenstern (2004).
DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ.
Nucleic Acids Research 32, W33-W36.

Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern:
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
Algorithms for Molecular Biology 2008, 3:6

SigniSite 2.1 – Residue level Genotype Phenotype Correlation in Protein Multiple Sequence Alignments

SigniSite 2.1

:: DESCRIPTION

SigniSite performs residue level genotype phenotype correlation in protein multiple sequence alignments by identifying amino acid residues significantly associated with the phenotype of the data set.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W286-91. doi: 10.1093/nar/gkt497. Epub 2013 Jun 12.
SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.
Jessen LE1, Hoof I, Lund O, Nielsen M.

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.