Services: Evolution And Phylogeny

The AgroLD (Agronomy Linked Data) Knowledge Graph is a specialized RDF database that integrates genomic and genetic information in plant science.

A customised Galaxy instance for the genomic characterisation of microoganisms in particular and data intensive biomedical research in general.

BEAST 2 is an open-source software tool and platform designed for Markov chain Monte Carlo (MCMC)-based Bayesian inference of phylogenetic trees and associated population-level (i.e. phylodynamic) parameters from (primarily) genetic sequence data under a large variety of specific models.

BUSCO provides quantitative measures for the assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Using BLAST score analysis to identify orthologous genes in large groups of related genomes

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images: it allows users to upload, and download and reprocess the thousands of raw, 2D images used to build a 3D structure.

Produces and maintains automatic and manually curated annotation on eukaryotic genomes. It is integrated with important molecular resources, for example UniProt, and can be accessed programmatically or through a web browser.

Provides access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces based on the Ensembl software platform.

Enterotypes are densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. Computational methods to detect and characterise enterotypes in any dataset, either to reproduce previous reports or determine enterotypes in new studies, are provided and explained. Part of the Microbiome Analysis Toolbox. 

European Search Catalogue for Plant Genetic Resources, information about 1.9 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes.

eggNOG is a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. eggNOG provides orthologous group assignments at >100 different taxonomic levels as well as multiple sequence alignments, maximum-likelihood trees and broad functional annotations for each group accessible via a web interface or through bulk download. Part of the Microbiome Analysis Toolbox.

Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

Database of human mitochondrial genomes from primary INSDC databases, personal submissions and application of MtoolBox to NGS data.

A comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. KnetMiner is a web application to search and visualise genome-scale knowledge networks. It is used by scientists in academia and industry to accelerate gene-trait discovery research. KnetMiner offers features such as keyword, gene list and genome region search, query refinement, gene ranking, gene set enrichment analysis and interactive visualisation of knowledge networks and genomic information.

A web tool and a mobile app for exploring the entire Tree of Life

A public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. 

A compilation of tools offering identification and quantification of microorganisms, working with cellular pathways, phylogenetic trees and microbial communities, including: 

• MOCAT - a modular and scalable software pipeline for analyzing shotgun metagenomics datasets generated with Illumina technology. 
• mOTUs - Metagenomic operational taxonomic units (mOTUs) allow for the quantification of known (sequenced) and unknown microorganisms at species-level resolution from shotgun sequencing data. 
• SIAMCAT -  a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. 
• eggNOG - a database of nested orthologous gene groups (NOGs) infered using unsupervised clustering applied to >2,000 complete genomes followed by comprehensive characterization and analysis of the resulting gene families. 
• Enterotyping - uses computational methods to detect and characterise densely populated regions in a high-dimensional space of microbiome community composition, by which human individuals can be stratified. 
• iPATH - a web-based tool for the visualization and analysis of cellular pathways. Based on current annotations (such as KEGG), it provides pathway maps for primary cellular metabolism as well as for some additional secondary metabolite synthesis and regulatory pathways. 
• iTOL - Interactive Tree Of Life (iTOL) is an online tool for the display and manipulation of phylogenetic trees. 

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. This resource supports COVID-19 / SARS-CoV-2 research.

OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year. 

OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. 

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.

REALPHY - The Reference sequence Alignment based Phylogeny builder is a free online pipeline that can infer phylogenetic trees from whole genome sequence data. The user only has to provide genome sequences in FASTA, GenBank or FASTQ formats. From these sequences phylogenetic trees are inferred via PhyML. The alignments, tree files and information on SNPs and deleted sites are available for download after the analysis is finished.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Data Analysis service for ribosomal RNA

SulfAtlas is a knowledge-based database which (i) helps to better annotate sulfatases in (meta)genomic data and notably to improve the prediction of substrate specificities; (ii) guides the experimental biologists to select target sulfatases which remain to be characterized in term of function and structure. The data contained in SulfAtlas is curated by experts, based on our phylogeny-based classification system and on literature.