ArboDraw 2006 – Phylogenetic Tree Builder & Viewer

ArboDraw 2006

:: DESCRIPTION

ArboDraw is a program for building and displaying phylogenetic trees of protein and nucleic acid sequences. It can import and display dendrogram files in Newick format (generated by MUSCLE, Phylip, clustalw, etc.). Among the key features are the ability to annotate sequences, and to select and color independently various parts of the tree. A very convenient annotation functionality allows the user to view annotations by placing the mouse above the sequence of interest. Edited and annotated files can be saved and restored at a later time.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ArboDraw

:: MORE INFORMATION

For comments, suggestions and bug reports contact the authors:

xiNET 1.1.13 – Crosslink Viewer

xiNET 1.1.13

:: DESCRIPTION

xiNET is an open source visualisation of cross-linking / mass spectrometry data. It provides an interactive 2D map of the cross-link network.

::DEVELOPER

Rappsilber Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PHP
  • Java

:: DOWNLOAD

 xiNET

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2015 Feb 3. pii: mcp.O114.042259.
xiNET: cross-link network maps with residue resolution.
Combe CW, Fischer L, Rappsilber J

jvenn 1.7 – An Interactive Venn Diagram Viewer

jvenn 1.7

:: DESCRIPTION

jvenn is a plug-in for the jQuery Javascript library. It is an integrative tool for comparing lists with Venn Diagrams

::DEVELOPER

jvenn team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript

:: DOWNLOAD

 jvenn

:: MORE INFORMATION

Citation

jvenn: an interactive Venn diagram viewer.
Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C.
BMC Bioinformatics. 2014 Aug 29;15:293. doi: 10.1186/1471-2105-15-293.

APP 2.30 – Pathway Viewer

APP 2.30

:: DESCRIPTION

APP (Advanced Pathway Painter)visualizes pathways (KEGG, GenMAPP, BioCarta…). The user has the possibility to display any kind of quantitative data from gene and protein experiments (e.g. microarrays from affymetrix) directly within the pathways (colours represent the value). The linking between the pathway items and the experiment data is done over the gene or protein names and their accession numbers. Furthermore the user has a quick overview on the gene/protein with the collected links in the web-interface。

::DEVELOPER

GSA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

APP

:: MORE INFORMATION

Mview 1.67 – Multiple Alignment Viewer

Mview 1.67

:: DESCRIPTION

Mview is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed.

Mview Online

::DEVELOPER

European Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Mview

:: MORE INFORMATION

Citation:

Bioinformatics. 1998;14(4):380-1.
MView: a web-compatible database search or multiple alignment viewer.
Brown NP, Leroy C, Sander C.

AliView 1.27 – Alignment Viewer and Editor for large data sets

AliView 1.27

:: DESCRIPTION

AliView is an alignment viewer and editor designed to meet the requirements of next generation sequencing era phylogenetic datasets.

::DEVELOPER

Anders Larsson

:: SCREENSHOTS

AliView

:: REQUIREMENTS

  • Linux /Windows/ MacOsX

:: DOWNLOAD

 AliView

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 5. pii: btu531.
AliView: a fast and lightweight alignment viewer and editor for large data sets.
Larsson A.

inGeno 0.6 – Integrated Genome and Ortholog Viewer

inGeno 0.6

:: DESCRIPTION

inGeno is designed for genome sequence comparisons, which has been proven to be powerful, in particular to prokaryotic genomes of close phylogenetic distances. The original purpose of this software is to user-friendly visualize the corresponding relationships between orthologous genes. Step by step, a series of algorithms are implemented and integrated together, thus enable a noise-reducing process, a locus collinear block recognition and a text-mining step, which are helpful for users to extract biological information precisely.

::DEVELOPER

Department of BioinformaticsUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 inGeno

:: MORE INFORMATION

Citation

inGeno–an integrated genome and ortholog viewer for improved genome to genome comparisons.
Liang C, Dandekar T.
BMC Bioinformatics. 2006 Oct 20;7:461.

ZMap 2.8.0 – Genome Browser

ZMap 2.8.0

:: DESCRIPTION

ZMap is a genome browser written in C with the aim of providing fast access to high volume data. Data may be requested from a variety of disparate sources in parallel and cached locally allowing new tracks to be loaded or the view of current data adjusted without delay. Multiple views of the data may be presented and tracks configured for different levels of detail.

::DEVELOPER

the Annotools team at the Sanger Institute zmap@sanger.ac.uk

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ZMap 

:: MORE INFORMATION

svviz 1.5.2 – A Read Viewer for Validating Structural Variants

svviz 1.5.2

:: DESCRIPTION

svviz visualizes high-throughput sequencing data relevant to a structural variant.

::DEVELOPER

Noah Spies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 svviz

:: MORE INFORMATION

Citation

svviz: a read viewer for validating structural variants.
Spies N, Zook JM, Salit M, Sidow A.
Bioinformatics. 2015 Aug 18. pii: btv478

RNAfamily – Java Viewer for RNA Secondary Structures

RNAfamily

:: DESCRIPTION

RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNAfamily

:: MORE INFORMATION

For questions about RNAfamily or for bug reports, please contact Helene Touzet