ProSeqViewer 1.0.42 – Visualize Sequence and Multiple Sequence Alignment (MSA)

MSA is a reproducible pipeline designed to assign signatures of different mutation types on a single-sample basis, using Non-Negative Least Squares method with optimisation based on configurable simulations.

::DEVELOPER

Sergey Senkin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MSA

:: MORE INFORMATION

Citation

Senkin S.
MSA: reproducible mutational signature attribution with confidence based on simulations.
BMC Bioinformatics. 2021 Nov 4;22(1):540. doi: 10.1186/s12859-021-04450-8. PMID: 34736398; PMCID: PMC8567580.

MSA 4.05 – Microsatellite Analyzer

MSA 4.05

:: DESCRIPTION

The MSA software tool was designed to handle large microsatellite data sets. To avoid error prone reformatting, MSA uses a simple input format, very close to a simple spreadsheet.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

MSA

:: MORE INFORMATION

Citation:

Dieringer, Daniel & Schlötterer, Christian (2003)
Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets.
Molecular Ecology Notes 3 (1), 167-169

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.

aRNhAck 1.0 – Prediction of RNA-binding interfaces using SHAPE data and MSA

aRNhAck 1.0

:: DESCRIPTION

aRNhAck is a software which illustrates the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces.

::DEVELOPER

Computer Science and Biology at McGill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

aRNhAck

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2016 Jun 20;44(11):e104. doi: 10.1093/nar/gkw217. Epub 2016 Apr 19.
Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.
Reinharz V1, Ponty Y2, Waldispühl J3.