BEAGLE Utilities 2013
:: DESCRIPTION
BEAGLE Utilities is a collection of utility programs for manipulating large data files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows / MacOsX
- Java
:: DOWNLOAD
:: MORE INFORMATION
Tag: Manipulate
Burntrees 0.3.3 – Perl script for manipulating MrBayes tree and Parameter files
Burntrees 0.3.3
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/ MacOsX
- Perl
:: DOWNLOAD
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / MacOsX / Linux
- Perl
:: DOWNLOAD
:: MORE INFORMATION
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
:: SCREENSHOTS
:: REQUIREMENTS
- Linux / Windows / MacOsX
- Java
:: DOWNLOAD
:: 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
:: 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
setsApp 2.2.0 – Save and Manipulate Sets of Nodes and Edges
setsApp 2.2.0
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
- Windows/Linux/MacOsX
- Java
- Cytoscape
:: DOWNLOAD
:: 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.
seg-suite – Manipulate Segments and Alignments
seg-suite
:: DESCRIPTION
The seg suite provides tools for manipulating segments and alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux
- C++ compiler
:: DOWNLOAD
:: 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
:: 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
Picard 2.25.5 – Manipulate SAM files
Picard 2.25.5
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / Linux / MacOSX
- Java
:: DOWNLOAD
:: MORE INFORMATION
3D Molecular Models 1.1.2 – Manipulate 3D Models of Molecules for Android
3D Molecular Models 1.1.2
:: DESCRIPTION
3D Molecular Models is an application that allows you to view, rotate … manipulate 3D models of molecules that all we ever heard or studied, besides giving us interesting details about them.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Android
:: DOWNLOAD
:: MORE INFORMATION
