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.

DNAscan 0.1 – Personal Computer compatible NGS Analysis, Annotation and Visualisation

DNAscan 0.1

:: DESCRIPTION

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

::DEVELOPER

DNAscan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DNAscan

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2019 Apr 27;20(1):213. doi: 10.1186/s12859-019-2791-8.
DNAscan: personal computer compatible NGS analysis, annotation and visualisation.
Iacoangeli A et al.

MIDAS 1.0 – Analysis and Visualisation of Interallelic Disequilibrium between Multiallelic Markers

MIDAS 1.0

:: DESCRIPTION

MIDAS (Multiallelic Interallelic Disequilibrium Analysis Software) is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers.

::DEVELOPER

The Bristol Genetic Epidemiology Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Mac OsX / Windows
  • Python

:: DOWNLOAD

 MIDAS

:: MORE INFORMATION

Citation:

Tom R Gaunt, Santiago Rodriguez, Carlos Zapata, Ian NM Day
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers.
BMC Bioinformatics 2006, 7:227 (27 April 2006)

iPiG r5 – Integrating PSMs into Genome Browser Visualisations

iPiG r5

:: DESCRIPTION

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser

::DEVELOPER

iPiG team

: SCREENSHOTS

iPiG

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • java

:: DOWNLOAD

  iPiG

:: MORE INFORMATION

Citation

iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations
Mathias Kuhring and Bernhard Y. Renard
PLoS ONE 7(12): e50246. doi:10.1371/journal.pone.0050246

SeqMonk 0.34.0 – Visualisation and Analysis of Mapped Sequence Data

SeqMonk 0.34.0

:: DESCRIPTION

SeqMonk is a program to enable the visualisation and analysis of mapped sequence data. It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 SeqMonk

:: MORE INFORMATION

DNAPlotter 1.11 – Circular & Linear Interactive Genome Visualisation

DNAPlotter 1.11

:: DESCRIPTION

DNAPlotter is a collaborative project between Jemboss and Artemis. It makes use of the existing circular plot in Jemboss and the Artemis sequence libraries.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

DNAPlotter

:: MORE INFORMATION

Citation

Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J
DNAPlotter: circular and linear interactive genome visualization.
Bioinformatics (Oxford, England) 2009;25;1;119-20

poRe 0.17 – An R package to enable Visualisation of Nanopore Sequencing data

poRe 0.17

:: DESCRIPTION

poRe (R_poRe) is a package for R that enables users to manipulate, organize, summarise and visualize MinION nanopore sequencing data.

::DEVELOPER

Mick Watson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 poRe

:: MORE INFORMATION

Citation

poRe: an R package for the visualization and analysis of nanopore sequencing data.
Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, Blaxter M.
Bioinformatics. 2014 Aug 29. pii: btu590.

Vivaldi – Visualisation, Analysis and Validation of NMR entries

Vivaldi

:: DESCRIPTION

Vivaldi is a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB).

::DEVELOPER

Protein Data Bank in Europe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB.
Hendrickx PM, Gutmanas A, Kleywegt GJ.
Proteins. 2013 Apr;81(4):583-91. doi: 10.1002/prot.24213

BioLayout Express3D 3.3 – Biological Network Visualisation and Analysis

BioLayout Express3D 3.3

:: DESCRIPTION

BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. Networks can be produced from a wide variety of relationships between entities. In biology this includes the interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. BioLayout Express3D has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data.

::DEVELOPER

The BioLayout Express3D team (support@biolayout.org)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 BioLayout Express3D 

:: MORE INFORMATION

Citation

Theocharidis A., van Dongen S., Enright A.J. and Freeman T.C.
Network Visualisation and Analysis of Gene Expression Data using BioLayout Express3D.
Nature Protocols 2009; Vol.4 No.10:1535-50.

Contiguity 1.0.4 – Contig Adjacency Graph Construction and Visualisation

Contiguity 1.0.4

:: DESCRIPTION

Contiguity is interactive software for the visualization and manipulation of de novo genome assemblies.

::DEVELOPER

Mitchell J Sullivan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Contiguity

:: MORE INFORMATION