Tag: phylogenomics

Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.

OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ort ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

HOGENOM is a phylogenomic database providing families of homologous genes and associated phylogenetic trees (and sequence alignments) for a wide set sequenced organisms.

HOVERGEN is a database of homologous vertebrate genes that allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees.

MetaPhOrs is a public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. Currently, over 117,131,162 of unique homologs are deposited in MetaPhOrs database. These ...

Hierarchy and modularity in evolving metabolic networks. Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online re ...

CUBAP (Codon Usage Biases Across Populations) is an interactive web portal for analyzing codon usage biases across populations. Although synonymous codon usage does not change the protein primary structure, codon choice significantly impacts translat ...

The Spirochetes Genome Browser

A collection of related protein sequences (clusters) consists of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses.

Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (htt ...

TAED is a database of phylogenetically indexed gene families. It contains multiple sequence alignments from MAFFT1, maximum likelihood phylogenetic trees from PhyML2, bootstrap values for each node, dN/dS ratios for each lineage from the free ratios ...