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