GenomeSignatureTree is a benchmark for alignment-free inference of genome trees. Unpack the downloaded file (tar xvfz GenomeSignatureTree.tar.gz on unix) and see the README file for details. Please note that this is a large file (114M). See Patil and McHardy 2013 for details.
taxator-tk is an algorithm and the accompanying software, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Please see Dröge et a. 2014" for details. The source code and issue tracker can be found at GitHub. We provide a set of example refpacks for use with taxator-tk.
PTree is a pattern-based, stochastic search method for maximum parsimony phylogenies. Please see Gregor, Steinbrueck and McHardy 2013 for details.
PARMA toolkit provides useful tools for handling short and error prone sequencing reads, e.g. produces by PAR-CLIP or HITS-CLIP. Those tools include error profile inference for an individual NGS dataset, an alignment processing pipeline based on the PARMA algorithm, combining alignments against multiple databases, simulating realistic PAR-CLIP reads and clustering aligned PAR-CLIP reads to identify RBP-bound regions. Please see Kloetgen et al. 2015 (under review) for details.
PhyloPythiaS is a fast and accurate sequence compositional classifier based on the structured output paradigm. It performes particularly well for taxonomic assignment of populations from novel genera, order or higher-level clades, when limited amounts of reference data were available. Accurate assignments could be performed based on 100 kb of training data for a sample population. Please see Patil et al. 2011 for details.
PhyloPythiaS+ A self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. Please see Gregor et al. 2014 for details.
Eden is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.
AdaPatch searches for dense and spatially distinct clusters of sites under positive selection on the surface of proteins. We suggest to apply it on protein structures of viruses of yet unknown adaptive behavior. This could identify further candidate regions that are important for host-virus interaction. Please see Tusche et al. 2012 for details.
AntigenicTreeTools infer antigenic trees to resolve the antigenic impact of amino acid changes mapped to individual branches of a phylogenetic tree. For sufficiently resolved branches, this allows to quantify the antigenic impact of single amino acid changes. However, the software is also applicable to problems where a phylogenetic tree and pair-wise phenotypic distances are available. Please see Steinbrueck and McHardy 2012 for details.
Refpacks for the Takator-tk application
Our paper "Critical Assessment of Metagenome Interpretation: the second round of challenges" is now online in Nature Methods. Datasets are available for available here for download.
GenoPheno web-server allows genotype-phenotype-specific machine-learning modelings. The input genomic features to Geno2Pheno can be provided by Seq2Pheno or directly by the user. It offers a wide range of configurable predictive models, optimization metrics, and validation approaches (e.g., tree-based cross-validation). Geno2Pheno then generates detailed performance overviews, publication-quality visualizations, optimized predictive models, and phenotype-specific biomarkers.
Traitar,the microbial trait analyzer. This is the Traitar web service for phenotyping bacteria based on their genome sequences.
This is the webapplication of taxator-tk! Taxator-tk performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
AdaPatch is a method for detecting positively selected patches of sites on the surface of viral proteins, which are likely candidates for being relevant for adaptive evolution.
PhyloPythias web service.