seg-suite – Manipulate Segments and Alignments

seg-suite

:: DESCRIPTION

The seg suite provides tools for manipulating segments and alignments.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 seg-suite

:: MORE INFORMATION

Picard 2.3.0 – Manipulate SAM files

Picard 2.3.0

:: DESCRIPTION

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

:: DEVELOPER

Picard Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Picard

:: MORE INFORMATION

JoinX 1.12.0 – Tool for Manipulating Genomic Data

JoinX 1.12.0

:: DESCRIPTION

Joinx is a lightweight tool for performing set operations (e.g., intersection, difference, …) on genomic data contained in .bed files. It also provides some limited analysis functions (concordance reports). An important assumption that joinx makes is that the input data is always sorted. This allows it to compute its results in an efficient manner.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JoinX

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2014 Mar 6;94(3):373-84. doi: 10.1016/j.ajhg.2014.01.016. Epub 2014 Feb 20.
Exome-based mapping and variant prioritization for inherited Mendelian disorders.
Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, Churchill JD, Buhr AC, Nutter N, Pierce EA, Blanton SH, Weinstock GM, Wilson RK, Daiger SP

setsApp 2.1.0 – Save and Manipulate Sets of Nodes and Edges

setsApp 2.1.0

:: DESCRIPTION

SetsApp is a Cytoscape 3 app allowing the user to create and manipulate sets of nodes or edges (but not sets with both nodes and edges, at least in the current version) in Cytoscape. Sets can be created for different networks.

::DEVELOPER

setsApp team

:: SCREENSHOTS

setsApp

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 SetsApp

:: MORE INFORMATION

Citation

setsApp: Set operations for Cytoscape Nodes and Edges.
Morris JH, Wu A, Doncheva NT, Albrecht M, Ferrin TE.
F1000Res. 2014 Jul 1;3:149. doi: 10.12688/f1000research.4392.1.

NGSCMD – A C program to Manipulate Next-generation Sequence data files

NGSCMD

:: DESCRIPTION

NGSCMD is a C program to manipulate next-generation sequence data files

::DEVELOPER

Laboratory for Comparative Population Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NGSCMD

:: MORE INFORMATION

BiNoM 2.5 – Cytoscape plug-in for Manipulating and Analysing biological networks

BiNoM 2.5

:: DESCRIPTION

BiNoM (Biological Network Manager )is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BiNoM

:: MORE INFORMATION

Citation:

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

Zinovyev A., Viara E., Calzone L., Barillot E.
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. 2008.
Bioinformatics 24(6):876-877

GO4J 1.1 – A Set of API used to Manipulate Gene Ontology Vocabulary

GO4J 1.1

:: DESCRIPTION

GO4J is a set of Java API to manipulate local GO (Gene Ontology) vocabulary. It has four features: parsing four kinds of GO defintion; organize all GO ids with directed graph; evaluating semantic similarity between any two GO ids; visualizing relations between any ids.

::DEVELOPER

 Guoqing Zhang

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GO4J

:: MORE INFORMATION

Scriptome – Protocols for Manipulating Biological Data

Scriptome

:: DESCRIPTION

The Scriptome is a set of tools that filter, format, and merge data in tabular or common biological formats. Use single tools to take a quick look at data, or string tools together in a protocol to explore the data more deeply.

::DEVELOPER

Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Perl

:: DOWNLOAD

 Scriptome

:: MORE INFORMATION

Chem3D for iPad 2.0.2 – View and manipulate stunning 3D chemical and biochemical images

 Chem3D for iPad 2.0.2

:: DESCRIPTION

Chem3D® for iPad is a free, structurally accurate molecular viewer for exploring and interacting with 3D models. Chem3D® can import 3D models with a wide variety of structural file types, and models can be rotated and scaled with the touch of finger to expose different viewpoints.

::DEVELOPER

PerkinElmer

:: SCREENSHOTS

Chem3D

:: REQUIREMENTS

  • iPad

:: DOWNLOAD

 Chem3D for iPad

:: MORE INFORMATION

Burntrees 0.2.2 – Perl script for manipulating MrBayes tree and Parameter files

Burntrees  0.2.2

:: DESCRIPTION

Burntrees is a script for manipulating tree (*.t, *.trprobs, *.con) and parameter (*.p) files from MrBayes (v.3). The script exctracts trees and (by default) the taxon translation table and the trailing “end;” from a MrBayes tree file.

::DEVELOPER

Johan Nylander 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 Burntrees

:: MORE INFORMATION