:: DESCRIPTION
MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ghurye, J., Treangen, T., Fedarko, M., Hervey, W. J., & Pop, M. (2019).
MetaCarvel: linking assembly graph motifs to biological variants.
Genome biology, 20(1), 1-14.
:: 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
MetaTISA is tool with an aim to improve translationa initiation sites (TISs) prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict TISs by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.
::DEVELOPER
ZhuLab, Peking Uiniversity, Beijing
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
Bioinformatics 2009,25(14):1843-1845.
:: DESCRIPTION
CoMeta is a tool used to assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.
CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S
:: DESCRIPTION
GWproxy is a software for clustering metagenome short reads. The software incorporates biological knowledge in the clustering process, by means of a list of proteins associated to
each read. These proteins are chosen from a reference proteome database according to their similarity with the given read, as evaluated by BLAST.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gianluigi Folino, Fabio Gori, Mike S. M. Jetten, and Elena Marchiori.
Clustering metagenome short reads using weighted proteins.
In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 7th European Conference, EvoBIO 2009, Tübingen, Germany, April 15-17, 2009, Proceedings, volume 5483 of Lecture Notes in Computer Science, pages 152-163. Springer, 2009.
:: DESCRIPTION
MLTreeMap is a tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments. Among these genes are protein coding phylogenetic markers, SSU rRNA genes and markers for important functional pathways.
::DEVELOPER
Christian von Mering (mering@imls.uzh.ch)
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MLTreeMap–accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.
Stark M, Berger SA, Stamatakis A, von Mering C.
BMC Genomics. 2010 Aug 5;11:461. doi: 10.1186/1471-2164-11-461.
:: DESCRIPTION
ShotgunFunctionalizeR is an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualising metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways.
::DEVELOPER
Erik Kristiansson (erik.kristiansson@neuro.gu.se) , Daniel Dalevi (daniel.dalevi@gmail.com)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kristiansson E, Hugenholtz P and Dalevi D. (2009).
ShotgunFunctionalizeR: An R-package for functional comparisons of metagenomes.
Bioinformatics. doi:10.1093/bioinformatics/btp508.
:: DESCRIPTION
cBar is a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
::DEVELOPER
the Computational Systems Biology Laboratory at the University of Georgia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fengfeng Zhou, Ying Xu
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Bioinformatics, 2010 26(16):2051-2052.
:: DESCRIPTION
Treephyler is a tool for fast taxonomic profiling of metagenomes. It combines the predictive power of tree-based and speed of signature-based approaches. Treephyler was evaluated on a real metagenome to assess its performance in comparison to previous approaches for taxonomic profiling.
::DEVELOPER
Department of Bioinformatics , University of Göttingen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
F. Schreiber, P. Gumrich , R. Daniel and P. Meinicke (2010)
Treephyler: fast taxonomic profiling of metagenomes
Bioinformatics 26, 960-961
