:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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)
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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
:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MSClust (Multi-Seeds Based Clustering Algorithm) is an Matlab package for Clustering 16S rRNA sequences into OTUs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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)
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
