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.

Mockrobiota – Public Resource for Microbiome Bioinformatics Benchmarking

Mockrobiota

:: DESCRIPTION

Mockrobiota is a public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

::DEVELOPER

Caporaso Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

Mockrobiota

:: MORE INFORMATION

Citation

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking.
Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG.
mSystems. 2016 Oct 18;1(5). pii: e00062-16

scikit-bio 0.5.5 – Python 3 package providing Data Structures, Algorithms and Educational Resources for Bioinformatics

scikit-bio 0.5.5

:: DESCRIPTION

scikit-bio is an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python

:: DOWNLOAD

scikit-bio

:: MORE INFORMATION

UGENE 33.0 – Integrated Bioinformatics Tools

UGENE 33.0

:: DESCRIPTION

UGENE is a visual environment for biomolecular research, integrating ever-growing set of bioinformatics algorithms.

::DEVELOPER

UniPro

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

 UGENE 

:: MORE INFORMATION

Citation

Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team.
Bioinformatics. 2012 Apr 15;28(8):1166-7. doi: 10.1093/bioinformatics/bts091. Epub 2012 Feb 24.

NCBI C++ Toolkit 22.0 – Collection of C++ Modules for Bioinformatics

NCBI C++ Toolkit 22.0

:: DESCRIPTION

NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications. NCBI C++ Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI.

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

NCBI C++ Toolkit

:: MORE INFORMATION

Citation

The NCBI C++ Toolkit Book [Internet].
Vakatov D, editor.

Bio++ 2.4.1 – C++ Libraries for Bioinformatics

Bio++ 2.4.1

:: DESCRIPTION

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is fully Object Oriented and is designed to be both easy to use and computer efficient.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

Bio++

:: MORE INFORMATION

Citation:

Dutheil J, Gaillard S, Bazin E, Glémin S, Ranwez V, Galtier N, Belkhir K.
Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics.
BMC Bioinformatics. 2006 Apr 4;7:188.

EMBOSS 6.6.0 / Jemboss 1.5 – Suite of Bioinformatics Tools

EMBOSS 6.6.0 / Jemboss 1.5

:: DESCRIPTION

EMBOSS (European Molecular Biology Open Software Suite) is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.

Jemboss is a graphical user interface to EMBOSS.

EMBOSS Online Version

::DEVELOPER

EMBOSS team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/ Linux
  • JAVA

:: DOWNLOAD

EMBOSS ; Jemboss

:: MORE INFORMATION

Citation:

EMBOSS: The European Molecular Biology Open Software Suite (2000)
Rice,P. Longden,I. and Bleasby,A.
Trends in Genetics 16, (6) pp276–277

Snakemake 3.7.1 – Scalable Bioinformatics Workflow Engine

Snakemake 3.7.1

:: DESCRIPTION

Snakemake is a workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.

::DEVELOPER

Johannes Köster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 Snakemake

:: MORE INFORMATION

Citation

Snakemake–a scalable bioinformatics workflow engine.
Köster J, Rahmann S.
Bioinformatics. 2012 Oct 1;28(19):2520-2.

BioShaDock – A Curated BioInformatics Container Registry

BioShaDock

:: DESCRIPTION

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images.

::DEVELOPER

BioShaDock team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BioShaDock

:: MORE INFORMATION

Citation

BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
Moreews F, Sallou O, Ménager H, Le Bras Y, Monjeaud C, Blanchet C, Collin O.
F1000Res. 2015 Dec 14;4:1443. doi: 10.12688/f1000research.7536.1. eCollection 2015.