TreeLign / FastTreeLign – Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics

TreeLign / FastTreeLign

:: DESCRIPTION

TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Perl

:: DOWNLOAD

 TreeLign

:: MORE INFORMATION

AbundantOTU+ 0.93b – Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA

AbundantOTU+ 0.93b

:: DESCRIPTION

AbundantOTU+ deals with sequences from rare species as well, compared to AbundantOTU!!

AbundantOTU is a software based on a Consensus Alignment (CA) algorithm,which infers consensus sequences, each representing an OTU,taking advantage of the sequence redundancy for abundant species. Pyrosequencing reads can then be recruited to the consensus sequences to give quantitative information for the corresponding species. As tested on 16S rRNA pyrosequence datasets from mock communities with known species, AbundantOTU rapidly reported identiffied sequences of the source 16S rRNAs and the abundances of the corresponding species.AbundantOTU was also applied to 16S rRNA pyrosequence datasets derived from real microbial communities and the results are in general agreement with previous studies.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 AbundantOTU+

:: MORE INFORMATION

Citation:

Yuzhen Ye.
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment.
The Proceedings of BIBM 2010, 153-157

PHYLOSHOP 1.01 – Predicts 16S rRNA Gene Fragments in Metagenomes

PHYLOSHOP 1.01

:: DESCRIPTION

PHYLOSHOP is a pipeline that predicts 16S rRNA gene fragments in metagenomes, reports the taxonomic assignment of these fragments, and visualizes their taxonomy distribution.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 PHYLOSHOP

:: MORE INFORMATION

Citation:

Neethu Shah, Haixu Tang, Thomas G. Doak and Yuzhen Ye.
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.
Pac Symp Biocomput. p:165-76 (2011)

16S classifier – Fast and Accurate Taxonomic Classification of 16S rRNA Sequences

16S classifier

:: DESCRIPTION

16S Classifier‘ is a Random Forest based tool which is developed to carry out fast, efficient and accurate taxonomic classification of 16S rRNA sequences. It has the unique ability to classify small Hypervariable Regions of 16S rRNA.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 16S classifier

:: MORE INFORMATION

Citation

16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.
Chaudhary N, Sharma AK, Agarwal P, Gupta A, Sharma VK.
PLoS One. 2015 Feb 3;10(2):e0116106. doi: 10.1371/journal.pone.0116106.

Tax4Fun 0.3.1 – Predicting Functional Profiles from Metagenomic 16S rRNA data

Tax4Fun 0.3.1

:: DESCRIPTION

Tax4Fun is a open-source R package that predicts the functional capabilities of microbial communities based on 16S datasets.

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 Tax4Fun

:: MORE INFORMATION

Citation

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P.
Bioinformatics. 2015 May 7. pii: btv287.

CATCh v1 – Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

CATCh v1

:: DESCRIPTION

CATCh is an ensemble classifier for chimera detection in 16S rRNA sequencing studies

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CATCh

:: MORE INFORMATION

Citation

Appl Environ Microbiol. 2015 Mar;81(5):1573-84. doi: 10.1128/AEM.02896-14. Epub 2014 Dec 19.
CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.
Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P

IPED v1 – Sequencing Error Correction in 16S rRNA Illmina paired-end Sequencing Reads

IPED v1

:: DESCRIPTION

IPED is a highly efficient denoising tool for Illumina paired-end 16S rRNA amplicon sequencing data.

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 IPED

:: MORE INFORMATION

MSClust 20130708 – Clustering 16S rRNA sequences into OTUs

MSClust 20130708

:: DESCRIPTION

MSClust (Multi-Seeds Based Clustering Algorithm) is an Matlab package for Clustering 16S rRNA sequences into OTUs.

::DEVELOPER

Zhao Hongyu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Matlab

:: DOWNLOAD

 MSClust

:: MORE INFORMATION

Citation

J Microbiol Methods. 2013 Sep;94(3):347-55. doi: 10.1016/j.mimet.2013.07.004. Epub 2013 Jul 28.
MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence.
Chen W1, Cheng Y, Zhang C, Zhang S, Zhao H.

ESPRIT 201102 – Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences

ESPRIT 201102

:: DESCRIPTION

ESPRIT is an algorithm for estimating species richness using large collections of 16S rRNA pyrosequences.

::DEVELOPER

Bioinformatics Laboratory, SUNY Buffalo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ESPRIT

:: MORE INFORMATION

Citation:

Y. Sun, Y. Cai, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie,
ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences,
Nucleic Acids Research, vol. 37, no. 10, e76, 2009. (impact factor: 7.8)

OrientationChecker 1.0 – Check Orientation of 16S rRNA Gene Sequences

OrientationChecker 1.0

:: DESCRIPTION

OrientationChecker is a simple tool for quickly locating the position of partial sequences within the 16S rRNA gene, and determining (and, if necessary, altering) their orientation, without the need for time-consuming multiple sequence alignments.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

OrientationChecker

:: MORE INFORMATION

Citation

KE Ashelford et al. (2006)
New Screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.
Applied and Environmental Microbiology, 72(9): 5734-5741.