Services: Software Tools

A collection of software solutions for pangenome analyses.

To searches user submitted sequences for any combination of Position Weight Matrices (PWMs), primary sequence patterns and structural motifs.

Software to identify defined fragments in biomacromolecules.

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.

Bioinformatics Docker Images Project, a library of over 50 Docker images. 

A platform for interpretation of proteomics identification results from multiple search engines.

Predictor of human deleterious Single Nucleotide Polymorphisms.

A binary classifier for predicting pathogenic variants in coding and non-coding regions.

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.

A phylogenetic inference platform for epidemiological investigations and population studies of bacterial pathogens.

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.

A suite of tools available on the web to predict and analyze protein structure, function and mutations. 

A human protein-protein interaction meta-database employing primary dataset integration via genetic information ontology, which allows the integrated network to be reversibly normalized to any level of genetic reference without loss of source information and enables primary PPI dataset cross-checking. The PICKLE web-based interface allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein or the gene level, at three PPI filtering modes.

Pipeline for Cancer Inference

A pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes.

PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. 

An environment for NGS data management and analytics

Web-interface and database providing tools for the management of different plant phenotyping platforms, and the analysis of images and data.

Annotation of plant reference genomes and pangenomes, support and consulting.

Platon detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. It analyses the distribution bias of protein-coding gene families among chromosomes and plasmids.

An open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables.

A method for estimating the localization of transmembrane proteins in polarized cells

PoseView automatically creates two-dimensional diagrams of complexes with known 3D structure according to chemical drawing conventions.

Post-Translational Modifications Mass Spectrometry Calculator (Emerging Service) 

A free web application that simplifies mass spectrometry calculations for post-translationally modified proteins.

Web application for protein-ligand binding sites analysis and visualization | This repositary contains PrankWeb web application.

An ML-based tool/web-server to (i) predict GPCR-G-protein couplings; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features

Tool for prediction of disease related mutations in proteins. Tool version 2 (PredictSNP 2) for prediction of disease related mutatins within human genome available since 2016.

Primer3 is a program for designing PCR primers and oligos. 

Tool for the detection of structurally similar protein binding sites and pairwise local structural alignment

PROGENy provides a function to infer pathway activity from gene expression. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signalling footprints in cancer gene expression

A complete, flexible analysis of protein microarrays for biomarker discovery. Part of the Proteomics Toolbox.