ENNB – Feature Selection and Comparison in Functional Analysis of Metagenomes

ENNB

:: DESCRIPTION

ENNB is a two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.In the first stage of the proposed procedure, the informative features are selected using Elastic Net as reducing the dimension of metagenomic data; in the second stage the differentially abundant features are detected using generalized linear models with a Negative Binomial distribution.

::DEVELOPER

Lingling An

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

ENNB

:: MORE INFORMATION

Citation

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.
Pookhao N, Sohn M, Li Q, Jenkins I, Du R, Jiang H, An L.
Bioinformatics. 2014 Sep 24. pii: btu635.

Nonpareil 3.3.4 – Estimate Average Coverage and Generate Nonpareil Curves

Nonpareil 3.3.4

:: DESCRIPTION

Nonpareil estimates the coverage of a Whole Genome Shotgun metagenome and generate projections of sequencing efforts.

::DEVELOPER

Environmental Microbial Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Mac / Linux

:: DOWNLOAD

Nonpareil

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):629-35. doi: 10.1093/bioinformatics/btt584. Epub 2013 Oct 11.
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.
Rodriguez-R LM1, Konstantinidis KT

CoMet-Universe – Fast Comparative Functional Profiling of Metagenomes

CoMet-Universe

:: DESCRIPTION

CoMet-Universe is a web-server for comparative analysis of metagenomes based on protein domain signatures

::DEVELOPER

Department of Bioinformatics , University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Aßhauer KP, Klingenberg H, Lingner T, Meinicke P.
Exploring neighborhoods in the metagenome universe.
Int J Mol Sci. 2014 Jul 14;15(7):12364-78. doi: 10.3390/ijms150712364. PMID: 25026170; PMCID: PMC4139848.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.
CoMet—a web server for comparative functional profiling of metagenomes.
Nucleic Acids Res. 2011

PhyloSift 1.0.1 – Phylogenetic and Taxonomic Analysis for Genomes and Metagenomes

PhyloSift 1.0.1

:: DESCRIPTION

PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.

::DEVELOPER

The Darling Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /MacOsX

:: DOWNLOAD

PhyloSift

:: MORE INFORMATION

Citation

PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA.
PeerJ. 2014 Jan 9;2:e243. doi: 10.7717/peerj.243.