| Abbr. | Full name | Functions | Publications |
| STRING |
Search Tool for the Retrieval of Interacting Genes/Proteins |
Analysis of known and predicted protein-protein interactions in all known genomes |
2019: STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
2017: The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
2006: STRING 7--recent developments in the integration and prediction of protein interactions.
2000: STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.
|
| SMART |
Simple Modular Architecture Research Tool |
Domain analysis |
2018: 20 years of the SMART protein domain annotation resource.
2006: SMART 5: domains in the context of genomes and networks.
1998: SMART, a simple modular architecture research tool: Identification of signaling domains
|
| eggNOG |
evolutionary genealogy of genes: Non-supervised Orthologous Groups |
a database of orthologous groups of genes |
2019: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
2016: eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
2014: eggNOG v4.0: nested orthology inference across 3686 organisms.
2008: eggNOG: automated construction and annotation of orthologous groups of genes.
|
| iPath |
Interactive Pathways Explorer |
interactive exploration of biochemical pathways and networks. |
2018: iPath3.0: interactive pathways explorer v3.
2011: iPath2.0: interactive pathway explorer.
2008: iPath: interactive exploration of biochemical pathways and networks.
|
| iTOL |
interactive Tree Of Life |
an online tool for the display and manipulation of phylogenetic trees. |
2016: Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
2007: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
|
| STITCH |
Search Tool for Interactions of Chemicals |
Database of known and predicted interactions of chemicals and proteins. |
2016: STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
2008: STITCH: interaction networks of chemicals and proteins.
|
| mOTU |
Metagenomic species profiling |
Metagenomics |
2019: Microbial abundance, activity and population genomic profiling with mOTUs2.
2013: Metagenomic species profiling using universal phylogenetic marker genes. |
| Microbiome-tools |
Microbiome Analysis Tools Developed at EMBL |
Microbiome Analysis |
2017 |
| NGLess |
NGS Processing with Less Work |
NGS data processing |
2017 |
| proGenomes |
A resource for consistent functional and taxonomic annotations of prokaryotic genomes. |
Genome Analsis |
2017: proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. |
| metaSNV |
A tool for metagenomic strain level analysis. |
metagenomic strain analysis |
2017: metaSNV: A tool for metagenomic strain level analysis. |
| MOCAT |
a metagenomic assembly, annotation and profiling framework. |
metagenomic assembly & annotation |
2016: MOCAT2: a metagenomic assembly, annotation and profiling framework.
2012: MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit.
|
| Suppl. to variablecomplexes |
Supplimentary information |
Protein complex stoichiometry |
2016: Spatiotemporal variation of mammalian protein complex stoichiometries. |
| CART |
a chemical annotation retrieval toolkit. |
Chemical annotation retrieval |
2016: CART-a chemical annotation retrieval toolkit. |
| ETE 3 |
Reconstruction, Analysis, and Visualization of Phylogenomic Data. |
Phylogeny |
2016: ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. |
| PTMcode |
A resource for functional associations of post-translational modifications within and between proteins. |
PTM analysis |
2015: PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
2013: PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins.
|
| Companion website |
Companion website for TaraOcean's paper |
TaraOcean Project |
2015: Structure and function of the global ocean microbiome. |
| Enterotyping |
Enterotyping : R tutorials |
Metagenomics |
2015: Enterotypes of the human gut microbiome. |
| SIDER |
The SIDER database of drugs and side effects. |
Drug side effects |
2013: Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding |
| CODIM |
Characterization of drug-induced transcriptional modules |
Drug-induced transcription modules |
2013: Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. |
| specI |
A species identification tool |
Prokaryotic species analysis |
2013: Accurate and universal delineation of prokaryotic species. |
| Chaetomium thermophilum genome resource |
The first complete genome of a true thermophilic eukaryote |
Genomics |
2011: Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. |
| iMyco |
Interactive Mycoplasma |
Interactive Pathways Explorer dedicated to Mycoplasma pneumoniae |
|
| Medusa |
|
a general graph visualization tool. Medusa will give users greater freedom in manipulating STRING data. |
Medusa: a simple tool for interaction graph analysis. |
| AQUA |
AQUA: automatic quality improvment for multiple sequence alignment: |
Alignment tool |
AQUA: Automated quality improvement for multiple sequence alignments. |
| PAL2NAL |
Sequence/Gene analysis |
Conversion of protein sequence alignments into the codon alignments + Ka/Ks-Calculations. |
Robust conversion of protein sequence alignments into the corresponding codon alignments. |
| PolyPhen |
Polymorphism Phenotyping |
prediction of functional effect of human nsSNPs |
Human non-synonymous SNPs: server and survey |
| BLAST2GENE |
|
Gene analysis in genomic regions |
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. |
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