Tag: Viewer

Belvu 20120403 – Multiple Alignments Viewer

Belvu 20120403

:: DESCRIPTION

Belvu is an X-windows viewer for multiple sequence alignments. One of the main advantages of Belvu is that it has an extensive set of modes to color the residues. There are several ways to color them by conservation and by residue type (user-configurable). Other useful features are fetching of the Swissprot (or PIR) entries by double clicking and easy tracking of the position in the alignment.

In addition, Belvu is a phylogenetic tool. It can be used to generate distance matrices between sequences under a selection of distance metrics. These can be saved and used subsequently in other applications. Belvu also implements certain distance-based tree reconstruction algorithms – including import of externally generated distance matrices – and bootstrap phylogenetic reconstruction. These functions are available both in the GUI (meaning Belvu may also be used as a tree viewer) or as command-line options, making the program a potential component in phylogenetic software pipelines.

::DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

Belvu

:: MORE INFORMATION

Citation:

“Scoredist: A simple and robust protein sequence distance estimator”
Erik LL Sonnhammer and Volker Hollich
BMC Bioinformatics 6:108 (2005)

EagleView 2.2 – Genome Assembler Viewer

EagleView 2.2

:: DESCRIPTION

EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.

::DEVELOPER

EagleView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 EagleView

:: MORE INFORMATION

Citation

Weichun Huang and Gabor Marth
EagleView: a genome assembly viewer for next-generation sequencing technologies,
Genome Res.,June 11, 2008

EvolView v3 – An Online Phylogenetic Tree Viewer and Customization Tool

EvolView v3

:: DESCRIPTION

EvolView is an easy-to-use online tool for displaying, managing and customizing phylogenetic trees.

::DEVELOPER

EvolView team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EvolView

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2019 Jul 2;47(W1):W270-W275. doi: 10.1093/nar/gkz357.
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.
Subramanian B, Gao S, Lercher MJ, Hu S, Chen WH.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W569-72. doi: 10.1093/nar/gks576. Epub 2012 Jun 13.
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.
Zhang H1, Gao S, Lercher MJ, Hu S, Chen WH

ggtree 2.0.0 – Phylogenetic Tree Viewer for Different Types of Tree Annotations

ggtree 2.0.0

:: DESCRIPTION

ggtree is a phylogenetic tree viewer for different types of tree annotations

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • Bioconductor

:: DOWNLOAD

 ggtree

:: MORE INFORMATION

Citation:

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*.
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.
Methods in Ecology and Evolution. 2017, 8(1):28-36

SylvX v.42 – A Viewer for Phylogenetic Tree Reconciliations

SylvX v.42

:: DESCRIPTION

SylvX is a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

SylvX

:: REQUIREMENTS

  • Windows/ MacOsX

:: DOWNLOAD

  SylvX

:: MORE INFORMATION

Citation

SylvX: a viewer for phylogenetic tree reconciliations.
Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V.
Bioinformatics. 2015 Oct 29. pii: btv625

FNV 1.0 – Light-weight Flash-based Network and Pathway Viewer

FNV 1.0

:: DESCRIPTION

FNV (Flashed-based Network Viewer) is for the visualization of small to moderately sized biological networks and pathways. FVN can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

FNV

:: REQUIREMENTS

  • Windows/Linux
  • Flash Player 

:: DOWNLOAD

 FNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1181-2. doi: 10.1093/bioinformatics/btr098. Epub 2011 Feb 23.
FNV: light-weight flash-based network and pathway viewer.
Dannenfelser R, Lachmann A, Szenk M, Ma’ayan A.

JSAV 2.0 – JavaScript Sequence Alignment Viewer

JSAV 2.0

:: DESCRIPTION

JSAV is a sequence alignment viewer written purely in JavaScript. It is extremely easy to include it in your code, but has many configuration options allowing you to control the functionality available to the user of your web site.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JavaScript

:: DOWNLOAD

  JSAV

:: MORE INFORMATION

Citation

F1000Res. 2014 Oct 23;3:249. doi: 10.12688/f1000research.5486.1. eCollection 2014.
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).
Martin AC

JTreeView 0.8 – Java based Phylogenetic Tree Viewer

JTreeView 0.8

:: DESCRIPTION

JTreeView is a basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees.

::DEVELOPER

JTreView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 JTreeView

:: MORE INFORMATION

svviz 1.4.0 – A Read Viewer for Validating Structural Variants

svviz 1.4.0

:: 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