Service list

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.

PhylomeDB is a public database for complete catalogs of gene phylogenie. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments.

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.

A comprehensive ontology for the plant domain, that is useful for data integration and querying heterogeneous data.

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

Providing a data and information resource for individual plant species

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.

Plant-oriented online resource for comparative, evolutionary and functional genomics.

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.

The Protein Model Database stores manually built 3D models of proteins.

Database of localization and post-translational modifications of transmembrane proteins in polarized cells

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

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation.

PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation and mailing lists.

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

A prediction system for GPI-anchored proteins.

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.

PRIDE (The Proteomics Identifications Database) is a standards-compliant, public repository for proteomics data. It contains protein and peptide identifications and their associated supporting evidence.

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

The Progenetix database provides an overview of mutation data in cancer, with a focus on copy number abnormalities (CNV / CNA), for all types of human malignancies.