Services: Software tools
Name of service | Tag | Related links* | Key collection | |
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MolMeDB |
MolMeDB is an open chemistry database about interactions of molecules with membranes. |
bio.tools | ||
MolStar |
Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. Can visualize also molecular dynamics. |
bio.tools | ||
MotiveValidator |
Web based application to validate ligand structure in PDB. |
bio.tools | ||
mOTUs |
Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. The method clusters single-copy phylogenetic marker gene sequences from metagenomes and reference genomes into mOTUs to profile their abundances in shotgun metagenomic samples. Part of the Microbiome Analysis Toolbox. |
bio.tools | ||
MS2PIP Server |
Tool to predict peptide fragment ion intensities for mass spectrometry-based proteomics data. |
bio.tools | ||
MToolBox |
A highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from NGS data. Predicts mitochondrial haplogroups. |
bio.tools | ||
MultiPLX |
A tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution. It uses nearest neighbour DNA binding thermodynamics to estimate unwanted pairings between PCR samples. |
bio.tools | ||
Network Analyzer |
A tool to visualize the output from the database for annotation, visualization and integrated discovery DAVID in order to reveal overlapping biological connections for a list of relevant genes. |
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Nextflow |
Enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. |
bio.tools | ||
NLP4BIA tools |
Textmining tools |
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Norine |
Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity. |
bio.tools | ||
Ocean Gene Atlas |
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences. |
bio.tools | ||
OMPdb |
OMPdb is a database of beta-barrel outer membrane proteins from Gram-negative bacteria. |
bio.tools | ||
OpenMS |
Mass Spec. analysis platform (See also Topp, LFQProfiler & RNPxl, MetaboProfiler) |
bio.tools | ||
OpenPepXL |
OpenMS tool for the study of Protein-Protein interactions. |
bio.tools | ||
Orange |
Open source software environment for development of biomedical data mining applications and data analysis workflows. |
bio.tools | ||
Orange4WS |
A service‐oriented environment for data mining, integrating web services as workflow components |
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Orione |
A Galaxy instance customized for data-intensive computational analyses in microbiology and metagenomics. |
bio.tools | ||
OTP |
OTP = "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing. The application provides support in all steps of this process, including data transfer from temporary to final storage, execution of data quality monitoring programs, alignment of reads to the reference genome and variant calling. It allows full automatization, extended project administration, and full processing control for operators. |
bio.tools | ||
Pasta |
Prediction of Amyloid STructure Aggregation is a web server predictor for amyloid aggregation propensity from protein sequences; |
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PatSearch |
To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs. |
bio.tools | ||
PatternQuery/PatternExplorer |
Software to identify defined fragments in biomacromolecules. |
bio.tools | ||
PCA-correlated SNPs tool |
Our algorithm for identifying PCA-correlated SNPs takes as input a properly encoded SNP data matrix and outputs a score for each SNP. SNPs corresponding to the highest scores are typically the most informative in reproducing the structure of the population. |
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Pegi3s |
Bioinformatics Docker Images Project, a library of over 50 Docker images. |
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PeptideShaker |
A platform for interpretation of proteomics identification results from multiple search engines. |
bio.tools | ||
PhD-SNP |
Predictor of human deleterious Single Nucleotide Polymorphisms. |
bio.tools | ||
PhD-SNPg |
A binary classifier for predicting pathogenic variants in coding and non-coding regions. |
bio.tools | ||
Phylogeny.fr |
phylogeny.fr is a web server intended to phylogenetic analyses.It has been designed to let non-specialist as well as expert users execute phylogenetic workflows. These workflows automatically chain programs to perform different tasks: the identification of homologous sequences, their multiple alignment, the alignment curation, the phylogenetic reconstruction and the graphical representation of the inferred tree. |
bio.tools | ||
PHYLOViZ |
A phylogenetic inference platform for epidemiological investigations and population studies of bacterial pathogens. |
bio.tools | ||
PhyML |
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements. |
bio.tools |