Tag: Java

BioJava 5.4.0 – Java Framework for Processing Biological Data

BioJava 5.4.0

:: DESCRIPTION

BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

::DEVELOPER

BioJava Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioJava

:: MORE INFORMATION

Citation:

BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494.

BioJava: an Open-Source Framework for Bioinformatics ,
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.
Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397.

JPrIME 0.3.7 – Bayesian Phylogenetics Library in Java

JPrIME 0.3.7

:: DESCRIPTION

JPrIME is a Java library with tools for phylogenetics. It is a complement to the the original C++ library PrIME

::DEVELOPER

JPrIME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • Java

:: DOWNLOAD

 JPrIME

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2994-5. doi: 10.1093/bioinformatics/bts548.
DLRS: gene tree evolution in light of a species tree.
Sjöstrand J, Sennblad B, Arvestad L, Lagergren J.

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

JABAWS 2.2 – JAva Bioinformatics Analysis Web Services

JABAWS 2.2

:: DESCRIPTION

JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview. JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Ronn and GlobPlot; and calculation of amino acid alignment conservation with AACon.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ Amazon EC2
  • Java

:: DOWNLOAD

 JABAWS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2001-2. doi: 10.1093/bioinformatics/btr304. Epub 2011 May 18.
Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA.
Troshin PV, Procter JB, Barton GJ.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOs
  • Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.

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

JDotter – Java Dot Plot Alignments

JDotter

:: DESCRIPTION

JDotter (Java Dot Plot Alignments) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JDotter

:: MORE INFORMATION

Citation:

Brodie, R., R. L. Roper, and C. Upton. 2004
JDotter: A Java Interface to Multiple DotPlots Generated by Dotter. Bioinformatics, 20, 279-281.

JAWAMix5 r2 – HDF5 based JAva implementation of Whole Genome Association Studies using Mixed models

JAWAMix5 r2

:: DESCRIPTION

JAWAMix5 is an out-of-core open-source toolkit for association mapping using high-throughput sequence data. Taking advantage of its HDF5-based implementation, JAWAMix5 stores genotype data on disk and accesses them as though stored in main memory. Therefore, it offers a scalable and fast analysis without concerns about memory usage, whatever the size of the dataset. We have implemented eight functions for association studies, including standard methods (linear models, mixed linear models, rare variants test, nested association mapping (NAM), and local variance component analysis), as well as a novel Bayesian local variance component analysis. Application to real data reveals new biological insights and demonstrates that JAWAMix5 is reasonably fast compared to traditional solutions that load the complete dataset into memory, and that the memory usage is efficient regardless of the dataset size.

::DEVELOPER

Quan Long

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • Java

:: DOWNLOAD

 JAWAMix5

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1220-2. doi: 10.1093/bioinformatics/btt122. Epub 2013 Mar 11.
JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models.
Long Q, Zhang Q, Vilhjalmsson BJ, Forai P, Seren ü, Nordborg M.

J/qtl 1.3.4 – Java GUI for R/qtl

J/qtl 1.3.4

:: DESCRIPTION

J/qtl is a Java graphical user interface (GUI) for the popular QTL data analysis software R/qtl.

::DEVELOPER

 Hao Wu, Lei Wu and Keith Sheppard.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 J/qtl 

:: MORE INFORMATION

Citation

Methods Mol Biol. 2009;573:175-88.
Quantitative trait locus analysis using J/qtl.
Smith R, Sheppard K, DiPetrillo K, Churchill G.

Periodic Tables Package 3.0 – Use Periodic Table on Computers

Periodic Tables Package 3.0

:: DESCRIPTION

The Periodic Tables Package is an advanced suite of applications for both Windows and Linux that allow chemists and students alike to use the Periodic Table on their computers.

::DEVELOPER

Amanda Burke

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Java

:: DOWNLOAD

 Periodic Tables Package

:: MORE INFORMATION

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