Tools 135 entries

Cryo-electron microscopy is currently one of the most active techniques in Structural Biology. The number of maps deposited …

3D-footprint: a database for the structural analysis of protein-DNA complexes

Bioinformatic annotations on macromolecular 3D structures

A network-based bioinformatics tool for generating libraries for fragment-based molecular replacement and for structure interpretation. The geometrical description …

Combining multiple partial solutions in reciprocal space. ALIXE combines information from multiple partial solutions to improve the starting …

AMIGO2 is a multi-platform MATLAB based toolbox designed to solve mathematical optimization problems which are at the core …

ANISE (grAphical coNfigurator of TIFOSI In Silico Experiments) is a web app to easily create/edit the XML configuration …

APID Interactomes provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration …

ARAMIS is an Accurate long-Reads Assembly correction Method for Indel errorS (ARAMIS), the first NGS long-reads indels correction …

Crystallographic ab initio protein solution below atomic resolution. Ab initio macromolecular phasing has been traditionally limited to small …

Python script that predicts the allergenicity of a plant protein with an SVM model trained to distinguish plant …

Avida is the most widely used Artificial Life software platform for studying evolutionary processes, in which self-replicating computer …

Tool to search the position of barley genetic markers on the Barley Physical Map and the POPSEQ map

BEHAV3D is a comprehensive platform combining multi-color live 3D imaging with computational analysis to study tumor-immune interactions. BEHAV3D …

BEHAV3D Tumor Profiler (BEHAV3D-TP) is a cloud-based computational platform designed to comprehensively map and analyze the dynamic heterogeneity …

Behavior-Guided Transcriptomics (BGT) is an extension of the BEHAV3D platform that links T cell live imaging with single-cell …

Machine-learning-based segmentation and lineage tracking of dense bacterial populations using Fiji (ImageJ) as a front-end. It leverages the …

Web server that finds biological features (qualitative or quantitative) over-represented in a user-given set of prokaryotic organisms compared …

Breaking-Cas is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications.

CODfinder.R is a TopDom-based software for identifying Coexpression Domains (CODs) using an expression matrix as input

Since the COVID-19 outbreak many molecular structure models, have been generated to identify new therapeutic targets to overcome …

Code to explore the cell types involved in rare disease phenotypes, using healthy single-cell RNA-seq reference atlases (Human …

A Contrastive Multi-Modal learning model with Biologically Informed Priors!

Browse millions of relationships between biological entities extracted from the scientific literature.

DeCovid is a Shiny app designed for exploring basal expression level differences between demographic risk factors, such as …

Tackling climate change challenges requires replacing current chemical industrial processes through the rational and sustainable use of biodiversity …

Python package for building, comparing, annotating, manipulating and visualising phylogenetic trees.

EasyGDB is a system designed to simplify the implementation of genomics portals and expression atlases, minimizing their maintenance.

Even though ecological interactions among microbes are fundamental for ecosystem functioning, most of them remain unknown. High-throughput omics …

Tools for evolutionary accumulation, or monotonic accumulation, models, known in cancer as "Cancer Progression Models".

Pipeline for functional annotation of proteins using language models

Catalogue and online browser of 404,085 functionally and evolutionarily significant novel (FESNov) gene families unique to uncultivated prokaryotic …

FIESTA 2.0 converts any table into an interactive system (FIESTA Viewer), allowing users to filter and sort data …

FLYCOP (FLexible sYnthetic Consortium OPtimization)

This web service is for the structural prediction of protein-protein interactions using an improved version of our Fast …

GEARS (Global parameter Estimation with Automated Regularisation via Sampling) is a MATLAB toolbox for parameter estimation in nonlinear …

A versatile software package for pan-genome analysis

An R package to calculate BLUP of the Genotype by environment metrics.

GWideCodeML is a Python package designed to facilitate genome-wide testing of evolutionary hypotheses using codeml, a tool from …

The Galaxy-SynBioCAD portal is a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows …

Web tool to visualise the genomic context (neighbourhood) of prokaryotic genes from a functional and evolutionary perspective, helping …

GenSSI 2.0 (Generating Series for testing Structural Identifiability) is a toolbox for structural identifiability analysis of linear and …

Gene selection with random forests.

Lipschitz-Killing Curvatures and Topological Data Analysis method for Machine Learning Image Classification (computer vision)!

Golden Standard (GS) is a Type IIS assembly method underpinned by the Standard European Vector Architecture. GS unlocks …

Improvement of Long Read Assemblies (ILRA) is a pipeline to help in the post assembly process (finishing) by …

Server for performing Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic …

Web server for biological interpretation of metabolomics data.

An updated version of the graphical user-friendly interface related to the Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) algorithm …

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

MEPSA: Minimum Energy Pathway Analysis for energy landscapes. A cross-platform user friendly tool for the analysis of energy …

MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces. An open source GUI-based program that natively calculates minimum …

Bulk and single-cell multi-omics ground truth simulator in R. The mosim function generates bulk transcriptomics data (RNA-seq) and …

Genomic Mating package. Optimize mating plans using genomic information to maximize genetic gain, within-family variance, and total genetic …

MirCure is a software for quality control, filtering, and curation of microRNA candidates. It evaluates miRNA-specific features based …

Graphical and interactive study of the co-evolution of two protein families and assessment of their interaction in a …

MorphoTrack-Merger is a Python-based tool designed to extract morphological features from segmented images and merge them with tracking …

Converts Biomart gene tables containing annotation terms (e.g. GO) into gmt files for Gene Set Enrichment Analysis (GSEA). …

NEMAT (Non-Equilibrium Membrane Alchemical Transformations) is an open-source framework designed to make non-equilibrium free-energy calculations for ligand binding …

NOISeq is a non-parametric tool for the analysis of differential expression in RNA-seq data

NeoAntigens Prediction@CNB (NAP-CNB) is a tool for the prediction of neoantigenic peptides from RNA-seq or protein data. It …

OliveAtlas aims to provide interactive bioinformatics tools to explore gene expression data of olive tree. The current version …

The Ontology for Avida (OntoAvida) aims to develop an integrated vocabulary for the description of Avida, the most …

It clusters sites along a biological sequence (genome or proteins) according to the values of the observables provided …

PC_ali performs hybrid multiple structure and sequence alignments based on the structure+sequence similarity score PC_sim. Besides the MSA, …

Summarises large sets of PubMed publications into an interactive local HTML report, where articles can be sorted and …

PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction) is an open-source, multi-platform tool for inferring network …

PROFILE is a tool designed to personalize patient-specific Boolean models using omics data. Boolean models are a type …

A web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. It supports …

Pathotypr is an alignment-free tool for harmonised Mycobacterium tuberculosis complex (MTBC) lineage assignment and resistance genotyping from assemblies …

Online platform to upload, annotate, visualise and share phylogenetic trees and multiple sequence alignments, from single Newick files …

Multiscale modelling tool used to simulate populations of cells and tissues

Statistical analysis of differential expression, including linear models and permutation tests

Fast protein loop modeling tool to efficiently generate loop ensembles.

A plant-dedicated server for the analysis of regulatory sequences

A comprehensive R pipeline for processing RNA-Seq datasets from count files (or tables) in non-model organisms comprising: Read/construct …

Software for Large-scale modelling of ecological communities with Lotka-Volterra models

RetroPath2.0 is an automated open source workflow for retrosynthesis based on generalized reaction rules that perform the retrosynthesis …

Expands partial polyalanine solutions by modelling side chains on the partial polypeptide trace with multiple sequence hypotheses, in …

SNPick is a fast and memory-efficient tool designed to extract SNP (Single Nucleotide Polymorphism) sites from large-scale FASTA …

SQANTI-SIM is a simulator of controlled transcript novelty for long-read RNA sequencing (lrRNA-seq) benchmarks. It allows users to …

Visualisation of SQANTI3 long-read defined transcriptomes in the UCSC Genome Browser: converts SQANTI3 outputs into interactive UCSC Track …

Read-level quality control framework for replicated long-read RNA-seq experiments, built on SQANTI3. The number and distribution of reads …

Tool for the quality control of long-reads transcript models

The framework SSCPE.pl infers Maximum Likelihood (ML) phylogenetic trees adoping the Structure and Stability constrained model of protein …

MATLAB toolbox for the automated, optimisation-based design of synthetic biological circuits, based on ODE models and mixed-integer nonlinear …

Workflow engine for Structural Biology and Bioinformatics

Scipion plugin. Base Scipion plugin defining objects and protocols for CHEMoinformatics and virtual drug screening.Scipion is a workflow …

Synthetic biology applies the principles of engineering to biology in order to create biological functionalities not seen before …

Allosteric transcription factor (aTF) based biosensors can be used to engineer genetic circuits for a wide range of …

SeqNjoy is a stand-alone application for generating and analyzing differential gene expression results from RNA-Seq experiments. Analyses can …

Molecular signatures with survival and censored data.

MATLAB code for a Graphic User Interface dedicated to automatically count and quantify dendritic spines from fluorescence microscopy …

Our web tool, S²-PepAnalyst, is designed to predict SSPs from input sequences or uploaded files (FASTA/FA/TXT) and identify …

Transcription Factor Enrichment Analysis Tool: Identifies transcription factor binding sites that are overrepresented in the regulatory regions of …

A Python library for dimensional reduction using topological auto-encoders

TiFoSi (Tissues: Forces and Signaling) simulates the dynamics of epithelial tissues in 2D. TiFoSi includes signaling (e.g. protein …

A class prediction and gene selection tool

Tomo3DEM is a software suite for in situ structural analysis of the subcellular architecture and molecular organization of …

R package for optimization of training populations in breeding programs.

Command-line tool that automates the annotation of large phylogenetic trees with metadata (categorical/numerical traits, NCBI/GTDB taxonomy, eggNOG-mapper output, …

Provides ways to inform AlphaFold predictions with additional and selected prior knowledge, through site-specific variants, predefined alignments and …

A Snakemake workflow for SARS-CoV-2 Viral Intra-Patient Evolution Reporting and Analysis. Viral mutations within patients nurture the adaptive …

An interactive tool for comparing lists using Venn Diagrams with support for up to 4 sets. Venny consists …

MATLAB toolbox for the visualisation of identifiability problems in dynamic biochemical models. It generates network files describing the …

Live online repository (a systematic review that anyone can contribute to) of computational tools that help researchers at …

Image processing algorithms for Cryo-Electron Microscopy

The program ZPeaks calls peaks from a genomic (NGS) experiment, comparing experiment and control over optimized windows.

Island-based MPI asynchronous enhanced parallel Differential Evolution algorithm. It adds a logarithmic search space, a local solver and …

Digital evolution is a branch of artificial life in which self-replicating computer programs—digital organisms—mutate and evolve within a …

bigMap is an improved unsupervised clustering protocol specially suited for large-scale structured data. The protocol follows three steps: …

Code to perform large-scale population dynamics simulations of species and resources.

Nextflow pipeline to demultiplex Oxford Nanopore reads that were multiplexed using Illumina dual-index identifiers. It runs in a …

eggNOGDB is a database for orthology functional annotations, eggnog-mapper is a tool based on eggNOGDB for fast genome-wide …

A database of transcription factors with annotated cis elements and binding interfaces

Community detection method for multiplex networks.

get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences. MNVs …

Assigns chemical compounds to biological pathways (KEGG, EnviPath, Reactome) using a profile-based approach, reporting z-scores and p-values and …

maSigPro is an R package for the analysis of transcriptomic time series data. The method is adapted to …

miARma is a fully customizable pipeline for NGS transcriptome analyses. Including gene/transcripts, miRNAs and circRNAs expression measurements.

miRGate is a curated database of human, mouse and rat miRNAs/mRNAs targets. It is designed to analyze miRNA …

The toolkit 'µSTASIS', or microSTASIS, has been developed for the stability analysis of microbiota in a temporal framework …

Ongoing tool to model population dynamics of bacteria with antimicrobials.

misosoup is a Python package for identifying minimal communities (minimal supplying community search). Through genome-scale constraint-based metabolic modeling, …

Genome Variability Analyses of multiple populations: Calculation and estimation of variability statistics and neutrality tests.

Detects significant protein co-evolution by computing p-values for tree-similarity correlations against a genome-wide background. Distributed as an academic …

Protein-protein docking pipeline using FFT-based sampling and energy-based scoring.

Protein-DNA docking.

Transcriptomic pipeline to automatically analyze entries from online databases or local raw data

saCMM (self-adaptive Cooperative Multimethod) is a parallel global optimisation library with several solvers based on scatter search and …

Global optimization library for computational systems biology.

saCeSS2 (Self-adaptive Cooperative enhanced Scatter Search 2) is a new version of the saCeSS library for large-scale mixed-integer …

tappAS is a free Java GUI application designed for the functional analysis of RNA-Seq data at the isoform …

A lightweight tool to find clusters of samples within a phylogeny. This command-line tool finds clusters of tips …

The program tnm computes the normal modes of protein structure <pdb1> in the space of torsion angles and …