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Showing 5 records out of 5 total
ChIP-Seq [Computational Cancer Genomics (P. Bucher)]
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Categories: genomics, (characterisation/annotation) - Software type(s): website, CLI - tool
The ChIP-Seq tools are used to analyze ChIP-seq data and other types of mass genome annotation data (MGA).The programs are: a feature correlation tool (ChIP-cor); a tag centering tool (ChIP-center); a signal peak detection tool (ChIP-peak and a partitioning tool (ChIP-part)
keywords: animal, arthropod, C, ChIP-seq, computer package, eukaryotic promoter, genomics, high-throughput, human, NGS, peak recognition, transcription factor binding site, transcription regulation, transcription start site annotation, vertebrate
FetchGWI / tagger [Vital-IT (I. Xenarios)]
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Categories: genomics - Software type(s): CLI - tool
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
keywords: alignment, animal, arthropod, C, computer package, human, insect, sequence analysis, sequence characterisation, short sequence alignment, vertebrate
MOSAIC Software Repository [MOSAIC (I. Sbalzarini)]
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Categories: systems biology, biophysics, imaging, IT infrastructure - Software type(s): CLI, library - tool
Various software for biomedical image processing and computational biology
keywords: C, HPC, ImageJ, image processing, interaction, Java, network, optimization, simulation
Newick Utilities [Computational Evolutionary Genomics (E. Zdobnov)]
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Categories: genomics, (sequence alignment), phylogeny/evolution - Software type(s): CLI - tool
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
keywords: C, filter, genomics, high-throughput, HPC, supertree, tree drawing, tree processing, tree reconstruction, visualization
Phylogibbs [Genome Systems Biology (E. van Nimwegen)]
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Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
keywords: alignment, alignment analysis, animal, arthropod, Bayesian network, binding sites prediction, C, ChIP-seq, evolution, fungi, genetic data analysis, genomics, Gibbs sampler, HMM, human, insect, interaction, maximum likelihood, model of evolution, multiple sequence alignment (MSA), network, NGS, phylogibbs, population genetics, regulatory site, selection, sequence analysis, sequence comparison, short sequence alignment, similarity search, transcription factor binding site, transcription module, transcription regulation, transcriptome analysis, vertebrate