Tag: phylogenetics

SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provide ...

The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based ...

The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). The GPCRDB contains data on sequences, ligand binding constants and mutations. ...

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

A public resource for knowledge on the timescale and evolutionary history of life.A search utility allows exploration of the thousands of divergence times among organisms in the published literature. A tree-based (hierarchical) system is used to iden ...

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 ...

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

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

A resource for exploring the evolution of protein function through relationships in sequence, structure, phylogeny and function.

Collaborative resource for the Bacillus community.

The ApiDB website (http://eupathdb.org/eupathdb) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center that integrates numerous database resources. The phylum Apicomplexa comprises numerous veterinary and med ...

Type II Toxin-Antitoxin loci in bacteria and archaea

Selectome is a database of positive selection, based on a branch-site likelihood test. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees.

GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.

Chaperonins are a diverse family of molecular chaperones present in the plastids, mitochondria, and cytoplasm of eukaryotes, and in bacteria and archaea. The family is divided into group I (CPN60, also known as Hsp60 or GroEL, found in bacteria, some ...

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.

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...

TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) re ...

The Prokaryotic Operon DataBase constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more th ...

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 ...

Predicted Arabidopsis Interactome Resource

Ortholog groups and trees for 66 proteomes inferred by Hieranoid 2

Comparative genomics of Fusarium strains

PmiREN is a comprehensive encyclopedia of plant miRNAs.

WDCM 10K sequencing projects

Voltage-gated potassium channel database

A comprehensive resource for the genes retained from whole genome duplication in vertebrates. The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison. A Repository of Genes Retained from Whole Genome Duplications in the Vert ...

Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization.

Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization.

Phylogenetic Exploration of Viruses and their Evolutionary Relationships

Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

A Comprehensive Hepatitis D Virus Database. Welcome to Hepatitis Delta Virus Database (HDVdb). The Hepatitis D Virus (HDV) Database, HDVdb contains comprehensive data on HDV genetic sequences that allows the researchers to investigate the genetic v ...

A new database designed specifically for Lactic Acid Bacteria bacteriocins | Bacteriocins from lactic acid bacteria (LAB) are successfully applied as natural alternatives to food preservation and to antibiotics; however, information on these antimicr ...

a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity da ...

Phylogenetic Oligonucleotide Probe Database. Provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes.

DBCOVP is a database of coronavirus virulent glycoproteins. A Knowledge Based Resource for Exploring the Functional and Immunological Properties of Coronavirus Virulent Glycoproteins for Application in Vaccine Target Discovery.

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. A high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosom ...

a genomic database of rice relatives for rice research | Welcome to RiceRelativesGD, a genomic database of rice relatives for rice research! | The cultivated rice (Oryza sativa) is one of the most important crops in the world

Server designed as a scientific tool for researchers to visualize their phylogenetic, biochemical, and immunological HA data in the three-dimensional context of the HA structure, in the hopes that the context may help researchers better interpret the ...

New open data resource for comparative studies of an old insect order. The Odonate Phenotypic DataBase is a resource for dragonfly and damselfly phenotypes. The database consists of a variety of morphological, behavioural, and bio-geographical infor ...

A database of Plant Chloroplast Inverted Repeats. Plant Chloroplast Inverted Repeats. Welcome to PCIR! Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables det ...

A database for the study of genomic reassortments among influenza viruses.

The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species.

an online database of unspecific peroxygenases. UPObase: Unspecific Peroxygenase Database : Homepage. Unspecific Peroxygenase Database (UPObase) is a genome mining pipeline based database which consists of all the sequences of fungal unspecific per ...

A comprehensive database for efficient retrieve and analysis of SNPs among 1210 maize lines. This R script chara-2-sparse.R is used to convert a traditional character genotype matrix into an integer sparse genotype matrix. This R script can be used ...

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 comprehensive mitochondrial genome database for Mollusca.

An integrated multi-omics database of barley gene families.

An integrative database of cancer-associated viruses.

A database of microorganisms and proteins linked to plastic biodegradation.

A Grameneae Genome Alignment Database of Homologous Genes Hierarchically Related to Evolutionary Events.

A webtool to identify and analyze bacterial microcompartment types in sequence data.

dbCNS is a database for conserved noncoding sequences.

A Database of Essential Genes Predicted Using Features From Interaction Networks.

This website contains implementations of the MGT for various species. The MGT and metadata is searchable to allow identification of GTs associated with spatial, temporal or clinical characteristics.

CarrotOmics is an integrated web-based relational database, developed to house and integrate genomic, genetic and breeding data for carrot and related species. CarrotOmics includes genome assemblies, annotated transcripts, traits, maps, and markers b ...

BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use ...

Morph·D·Base has been developed to serve scientific research and education. It provides a platform for storing the detailed documentation of all material, methods, procedures, and concepts applied, together with the specific parameters, values, techn ...