SAMStat 1.5.1 – Display Sequence Statistics for Next Generation Sequencing

SAMStat 1.5.1

:: DESCRIPTION

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SAMStat

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 1;27(1):130-1. doi: 10.1093/bioinformatics/btq614. Epub 2010 Nov 18.
SAMStat: monitoring biases in next generation sequencing data.
Lassmann T1, Hayashizaki Y, Daub CO.

Phy2HTML 1.0 – Display Phylogeny using only HTML and CSS

Phy2HTML 1.0

:: DESCRIPTION

Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Phy2HTML

:: MORE INFORMATION

iTOL 5.2 – Display & Manipulation of Phylogenetic Trees

iTOL 5.2

:: DESCRIPTION

iTOL (Interactive Tree Of Life) is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize mid-sized trees (up to several thousand leaves). Trees can be exported to several graphical formats, both bitmap and vector based.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser (Firefox)

:: DOWNLOAD

 iTOL

:: MORE INFORMATION

Citation

Interactive Tree Of Life (iTOL) v4: recent updates and new developments.
Letunic I, Bork P.
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259. doi: 10.1093/nar/gkz239.

Bioinformatics. 2007 Jan 1;23(1):127-8. Epub 2006 Oct 18.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic I, Bork P.

Letunic I and Bork P (2011)
Nucleic Acids Res doi: 10.1093/nar/gkr201
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

BamView 1.2.11 – Display of Read Alignments in BAM Data Files

BamView 1.2.11

:: DESCRIPTION

BamView is a free interactive display of read alignments in BAM data files.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

BamView

:: MORE INFORMATION

Citation

Brief Bioinform. 2013 Mar;14(2):203-12. doi: 10.1093/bib/bbr073. Epub 2012 Jan 16.
BamView: visualizing and interpretation of next-generation sequencing read alignments.
Carver T1, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA.

Tim Carver; Ulrike Böhme, Thomas D. Otto; Julian Parkhill; Matthew Berriman
BamView: Viewing mapped read alignment data in the context of the reference sequence.
Bioinformatics 2010;

PDBjViewer 4.4.4 – Display 3D Molecular Graphics of Proteins and Nucleic Acids

PDBjViewer 4.4.4

:: DESCRIPTION

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids.

::DEVELOPER

Kengo Kinoshita (Graduate School of Information SciencesTohoku University) and Haruki Nakamura (IPROsaka University)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java
  • JOGL

:: DOWNLOAD

 PDBjViewer

:: MORE INFORMATION

Citation

Bioinformatics. 2004 May 22;20(8):1329-30. Epub 2004 Feb 10.
eF-site and PDBjViewer: database and viewer for protein functional sites.
Kinoshita K, Nakamura H.

DNAlive – Display DNA Structural Features in relation with Genome Annotations and Functions

DNAlive

:: DESCRIPTION

 DNAlive displays DNA structure features in relation with genome annotations and functions.DNAlive is a tool for the analysis of structural and physical characteristics of genomic DNA.

::DEVELOPER

Molecular Modelling & Bioinformatics Unit. IRB Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 1;24(15):1731-2. Epub 2008 Jun 9.
DNAlive: a tool for the physical analysis of DNA at the genomic scale.
Goñi JR, Fenollosa C, Pérez A, Torrents D, Orozco M.

MOLDEN 5.4 – Package for Displaying Molecular Density

MOLDEN 5.4

:: DESCRIPTION

Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format.

::DEVELOPER

G.SchaftenaarCentre for Molecular and Biomolecular Informatics(CMBI), Radboud University Nijmegen Medical Centre

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 MOLDEN

:: MORE INFORMATION

Citation

J Comput Aided Mol Des. 2000 Feb;14(2):123-34.
Molden: a pre- and post-processing program for molecular and electronic structures.
Schaftenaar G, Noordik JH.

GSDS 2.0 – Gene Structure Display Server

GSDS 2.0

:: DESCRIPTION

GSDS is designed for the visualization of annotated features for genes, and the generation of high-quality figures for publication.

::DEVELOPER

Center for Bioinformatics(CBI), Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

GSDS 2.0: an upgraded gene feature visualization server.
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G.
Bioinformatics. 2014 Dec 10. pii: btu817

MapMan 3.6.0RC1 – Displays large datasets onto Diagrams of Metabolic Pathways

MapMan 3.6.0RC1

:: DESCRIPTION

MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology, Golm, Germany.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MapMan

:: MORE INFORMATION

Citation

Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY and M Stitt (2004)
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Plant J. 37(6):914-39.

Pairoscope 0.4.2 – Display of Paired End Reads

Pairoscope 0.4.2

:: DESCRIPTION

Pairoscope (formerly Yenta) was developed as a quick and simple way to generate diagrams indicating the relationship of paired end sequencing reads. It functions by displaying multiple genomic regions, their read depth at each base in the region and arcs within or between regions to indicate pairing information. Currently, Pairoscope supports the graphing of multiple regions, but they must be at different locations: the behavior of Pairoscope is undefined if attempting to graph the same region twice. It uses a bam file as input, and color codes the read pair graph to reflect different types of abnormally oriented reads. Individual reads are represented as vertical lines drawn at the genomic location where the read mapped.

::DEVELOPER

The Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Pairoscope

:: MORE INFORMATION