SIENA has been developed for the automated assembly and preprocessing of protein binding site ensembles.

Structural and physico-chemical interpretation of QSAR models

SQANTI3 is the first module of the [Functional IsoTranscriptomics (FIT)](https://tappas.org/) framework, which also includes IsoAnnot and tappAS.

Nextflow pipeline for splicing quantitative trait loci (sQTL) mapping based on sQTLseekeR2, performing the following analysis steps:

1. Index the genotype file
2. Preprocess the transcript expression data
3. Test for association between splicing ratios (a multivariate phenotype) and genetic variants in cis (nominal pass)
4. Obtain an empirical P-value for each phenotype (permutation pass, optional)
5. Control for multiple testing.

Software for Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation.

 SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. It provides the functionality of SSAMs most popular and widely used features in a graphical user interface with a few functions added for convenience and ease of use. It can be run on a modest laptop.

StructureProfiler is a tool to screen structures based on selection criteria typically used upon dataset assembly for structure-based design methods.

A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.

UseGalaxy.fr is the national Galaxy instance for ELIXIR-FR and deployed on the IFB Core Cluster and enabling reproducible analysis for french and international researchers in different domains: genomics, metagenomics, metabolomics, proteomics, ecology.

WarPP is a fully automated procedure to place water molecules in the active site of a protein structure.