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.

Galaxy 19.09 – Evolutionary and Data Processing Module Development

Galaxy 19.09

:: DESCRIPTION

Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.

::DEVELOPER

Galaxy Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux
  • Python

:: DOWNLOAD

 Galaxy

:: MORE INFORMATION

Citation

Genome Res. 2009 Nov;19(11):2144-53. Epub 2009 Oct 9.
Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team.

NYoSh Analysis Workbench 2.0 – Biological data analysis based on Meta Programming System

NYoSh Analysis Workbench 2.0

:: DESCRIPTION

NYoSh (Not your ordinary Shell) Analysis Workbench is a data analysis workbench built on top of MPS. Takes advantage of composable languages to create a platform intermediate between command line flexibility and user-friendly custom interfaces.

::DEVELOPER

Campagne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • Active MQ

:: DOWNLOAD

NYoSh Analysis Workbench

:: MORE INFORMATION

Citation

PeerJ. 2014 Jan 2;2:e241. doi: 10.7717/peerj.241. eCollection 2014.
Composable languages for bioinformatics: the NYoSh experiment.
Simi M, Campagne F.

MetaR 2.0.2 – Data Analysis with the R Ecosystem

MetaR 2.0.2

:: DESCRIPTION

MetaR (Metaprogramming in R) takes advantage of Language Workbench Technology to facilitate data analysis with the R language.

::DEVELOPER

Campagne Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

MetaR

:: MORE INFORMATION

Citation

Fabien Campagne, William ER Digan, Manuele Simi
MetaR: simple, high-level languages for data analysis with the R ecosystem
bioRxiv 2015 doi: http://dx.doi.org/10.1101/030254

Parallel-META 3.5.2 – A Parallel Metagenomic Analysis Pipeline

Parallel-META 3.5.2

:: DESCRIPTION

Parallel-META is a GPGPU and Multi-Core CPU based software which can parallelly analyze massive metagenomic data structures, report the classification, construction and distribution on phylogenetic & taxonomic and functional level.

::DEVELOPER

Bioinformatics Group , Single-cell Reseearch Center of Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences (QIBEBT-CAS).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • C Compiler
  • R

:: DOWNLOAD

 Parallel-META

:: MORE INFORMATION

Citation

Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization.
Su X, Pan W, Song B, Xu J, Ning K.
PLoS One. 2014 Mar 3;9(3):e89323. doi: 10.1371/journal.pone.0089323.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.
Su X, Xu J, Ning K.
BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16.

NG6 3.2 – Next Generation Sequencing Information System

NG6 3.2

:: DESCRIPTION

NG6 is an extensible sequencing provider oriented LIMS. It includes read quality control and first level analysis processes which ease the data validation made jointly by the sequencing facility staff ant the end-users. It provides a secured user-friendly interface to visualize and download the raw sequences files and the analysis results.

NG6 Online Version

::DEVELOPER

the bioinformatic and genomic plateforms of Genotoul.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • virtual machine

:: DOWNLOAD

 NG6

:: MORE INFORMATION

Citation

Mariette J, Escudie F, Allias N, Salin G, Noirot C, Thomas S, Klopp C.
NG6: Integrated next generation sequencing storage and processing environment.
BMC Genomics, 2012 13:462

IOBIO – Realtime Genomic Data Visualization and Analysis Web Tools

IOBIO

:: DESCRIPTION

Iobio provides free and open-source tools that help to generate gene list, variant interrogation, and more!

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

IOBIO

:: MORE INFORMATION

Citation

Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools.
Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT.
J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.

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

QIIME2 2019.10 – Analysis of Microbial Communities

QIIME2 2019.10

:: DESCRIPTION

QIIME (Quantitative Insights Into Microbial Ecology) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field.

::DEVELOPER

Knight LabJeff Werner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QIIME

:: MORE INFORMATION

Citation

J Gregory Caporaso et al.
QIIME allows analysis of high-throughput community sequencing data
Nature Methods, 2010; doi:10.1038/nmeth.f.303

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Bolyen E, et al.
Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9.

PyCogent 1.9 – Software Library for Genomic Biology

PyCogent 1.9

:: DESCRIPTION

PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. It is distinguished by many unique built-in capabilities (such as true codon alignment) and the frequent addition of entirely new methods for the analysis of genomic data.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 PyCogent

:: MORE INFORMATION

Citation

Knight et al., 2007,
PyCogent: a toolkit for making sense from sequence
Genome Biol, 8, R171.