Category: Microbiology

BioAtlas – Location-specific analysis of Microbial profiles

BioAtlas

:: DESCRIPTION

BioAtlas is a web service, primarily designed for biologists to explore where 16S rRNA strains classified from bacteria and/or archaea taxonomy are found, whether it be geographical and/or host-oriented locations.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Interactive microbial distribution analysis using BioAtlas.
Lund JB, List M, Baumbach J.
Nucleic Acids Res. 2017 Jul 3;45(W1):W509-W513. doi: 10.1093/nar/gkx304.

BURRITO – Visualization Tool for Exploratory Data Analysis of Metagenomic data

BURRITO

:: DESCRIPTION

BURRITO is a web-based tool for interactive exploration of metagenomic datasets, linking taxonomic and functional microbiome profiles

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

BURRITO

:: MORE INFORMATION

Citation

Front Microbiol. 2018 Mar 1;9:365. doi: 10.3389/fmicb.2018.00365. eCollection 2018.
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.
McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E.

CoMiDA v1.0.0 – Designing Minimal Microbial Communities with specified Metabolic Functions

CoMiDA v1.0.0

:: DESCRIPTION

CoMiDA is an algorithm for designing simple communities with some predefined metabolic capacities.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoMiDA

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Jul 1;32(13):2008-16. doi: 10.1093/bioinformatics/btw107.
An algorithm for designing minimal microbial communities with desired metabolic capacities.
Eng A, Borenstein E.

FishTaco 1.1.3 – Linking Taxonomic and Functional Shifts in the Microbiome

FishTaco 1.1.3

:: DESCRIPTION

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework, aiming to identify the taxa that are driving the functional shifts we observe in microbiomes of different individuals or disease states.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FishTaco

:: MORE INFORMATION

Citation

Cell Host Microbe. 2017 Feb 8;21(2):254-267. doi: 10.1016/j.chom.2016.12.014.
Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.
Manor O, Borenstein E.

NetCooperate – Determining Host-microbe and Microbe-microbe Cooperation

NetCooperate

:: DESCRIPTION

NetCooperate is a web tool and a software package for determining host-microbe and microbe-microbe cooperative potential.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 NetCooperate

:: MORE INFORMATION

Citation

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.
Levy R, Carr R, Kreimer A, Freilich S, Borenstein E.
BMC Bioinformatics. 2015 May 17;16:164. doi: 10.1186/s12859-015-0588-y.

GrowthRates 4.0 – Calculates Bacterial Growth Rates

GrowthRates 4.0

:: DESCRIPTION

GrowthRates is a program that calculates bacterial growth rates from the data generated by a micro-plate reader used to monitor the growth of bacterial cultures in micro-plate wells. The program automatically identifies the exponential phase of the growth curve and uses that portion of the curve to calculate growth rates and std. errors of those rates

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GrowthRates

:: MORE INFORMATION

Citation

Statistical Package for Growth Rates Made Easy.
Mira P, Barlow M, Meza JC, Hall BG.
Mol Biol Evol. 2017 Dec 1;34(12):3303-3309. doi: 10.1093/molbev/msx255.

EMPeror 1.0.0-beta.20 – Analysis of High Throughput Microbial Ecology datasets

EMPeror 1.0.0-beta.20

:: DESCRIPTION

Emperor is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

 EMPeror

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Numpy
  • qcli

:: DOWNLOAD

 EMPeror

 :: MORE INFORMATION

Citation

EMPeror: a tool for visualizing high-throughput microbial community data.
Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
Gigascience. 2013 Nov 26;2(1):16. doi: 10.1186/2047-217X-2-16.

E-vident – Elucidating Sampling Effort for Microbial Analysis Studies

E-vident

:: DESCRIPTION

Evident is a web-based software tool with an interactive user interface, implemented in HTML, Web Graphics Library, mod_python and QIIME. The interface of E-vident (Fig. 1) is comprised of: (i) the selection of parameters (i.e., study of interest, number of sequences per sample, the number of samples to use, and the number of iterations); (ii) the kind of visualizations to generate (Demo PCoA shows the original results from the study, and PCoA recalculates the study using the user-defined parameters in (i); (iii) the WebGL plot display.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

Evident

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Apache
  • QIIME
  • Python

:: DOWNLOAD

 E-vident

:: MORE INFORMATION

AXIOME 1.5 / AXIOMATIC – Exploration of Microbial Diversity

AXIOME 1.5 / AXIOMATIC

:: DESCRIPTION

AXIOME (Automation, eXtension, and Integration Of Microbial Ecology) is a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.

AXIOMATIC is a GUI companion for AXIOME

::DEVELOPER

AXIOME team

:: SCREENSHOTS

AXIOME

:: REQUIREMENTS

  • Linux / MacOsX
  • QIIME
  • Python

:: DOWNLOAD

 AXIOME , AXIOMATIC

:: MORE INFORMATION

Citation

AXIOME: automated exploration of microbial diversity.
Lynch MDj, Masella AP, Hall MW, Bartram AK, Neufeld JD.
Gigascience. 2013 Mar 13;2(1):3. doi: 10.1186/2047-217X-2-3.