Tag: phylogeny

Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

The Dfam database is a open collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations. Dfam represents a collection of multiple sequence alignments, each containing a set of r ...

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, anal ...

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.

ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.

The Hymenoptera Genome Database (HGD) is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD is divided into three main divisions: BeeBase, which hosts bee genomes and the Bee Pes ...

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 ...

Gypsy database of mobile genetic elements

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 ...

Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

Voltage-gated potassium channel database

Database of all currently available Symbiodinium sequences and associated host information of data collected from the Great Barrier Reef into a single relational database.

Repository for well-characterized elastin sequences to facilitate its study. The database has since expanded to include other non-elastin sequences that share elastic properties.

Phylogenetic Exploration of Viruses and their Evolutionary Relationships

Fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences.

The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) is a database of barcoded Chytridiomyceta and Blastocladiomycota cultures.

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis | Non-specific lipid transfer protein structure modeling | Theoretical structures have been calculated for the ...

PPNID: a manually curated reference database and identification tool for plant-parasitic nematode.

WARPP is the Web Application for the Research of Parasitic Plants, a community hub for access, information sharing and analysis of parasitic plant-specific data. The aim of this resource is to facilitate international efforts for the study of parasit ...

A database of somatic mutations in normal human tissues.

WCO-Lite is an online nomenclatural catalogue of harvestmen of the world (Arachnida, Opiliones) curated in TaxonWorks.

The Organonitrogen Degradation Database (ONDB) is used to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds.

ResiDB is a user-friendly sequence similarity-dependent database manager for bacteria, fungi, viruses, protozoa, invertebrate, plants, archaea, environmental and whole genome shotgun sequence data. Create a new database Access existing databases Loa ...

Computational prediction of animal microRNA genes

The Ligand-Gated Ion Channel database provides access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamat ...

A database of the phylogeny and physiology of thermophilic and hyperthermophilic organisms.

Phylogenize is a web tool that allows users to link microbial genes to environments, accounting for phylogeny. More specifically, given community composition data, phylogenize links genes in microbial genomes to either microbial prevalence in, or sp ...

EMBF is a database of enzymes of microalgal biofuel feedstock.

A Comprehensive Protein-coding Gene Origination Database on the Evolutionary Timescale of Life.

A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.

FishmiRNA is an evolutionarily-supported, manually-curated, genome duplication-aware database for the annotation of ray-finned fish miRNA genes, their mature products and their expression profiles.

ProModb (Protein interaction-based functional Module database) is a repository that documents computationally generated whole-cell protein-protein interaction network-based functional modules of an organism.

proMGE is a resource for the retrieval of 6 Mobile Genetic Element (MGE) categories in 76K genomes (totalling to 2.4 million prokaryotic MGEs) and classification of new ones in user provided protein sequences from genomes and genomic fragments.

A21 Retrospectively describing hepatitis C virus transmission dynamics and tracking HCV transmission networks in real-time for strategic elimination interventions | Real-time tracking of pathogen evolution | Nextstrain is an open-source project to ha ...

A comprehensive organelle genomes database for algae cpDNA and mtDNA. Algae is the earliest evolutionary biological group on the earth, are thought to have appeared at least 2.6 billion years ago. As the most complex biological group, algae have sho ...

The DSMZ is the most comprehensive biological resource center worldwide. Being one of the world's largest collections, the DSMZ currently comprises more than 73,700 items, including about 31,900 different bacterial and 6,600 fungal strains, 840 human ...