GGDC.md

title	description	published	date	tags	editor	dateCreated
Genome-to-Genome Distance Calculator (GGDC)	A collection of tools involved in virus/prokaryotic taxonomy, phylogeny, and genome comparison	true	2020-10-14 14:44:55 UTC	genomes, taxonomy, 2019, phylogeny, 2017, 2013, virus	markdown	2020-08-05 14:38:39 UTC

Genome-to-Genome Distance Calculator (GGDC)

Genome Sequence-Based (Sub-)Species Delineation. The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C content.

Genome-Based Phylogeny and Classification of Phages. Advanced comparison of bacterial and archaeal viruses using their genome or proteome sequences. Results include phylogenomic trees with branch support, suggestions for the classification and publication-ready text.

Inference of Gene Phylogenies and Gene Similarities. Calculate phylogenetic trees and pairwise gene sequence similarities from 16S rRNA or other genes using state-of-the-art methods. {.is-info}

Website

• GGDC Home Page
• GGDC GGDC tool
• TYGS TYGS tool
• VICTOR VICTOR tool
• Phylogeny Service Single gene tree tool {.links-list}

Notes from the user

GGDC tool, Genome-to-Genome Distance Calculator 2.1

• Only works with NCBI ids.

TYGS tool, Type (Strain) Genome Server

• Gives a lot of results to analyse to decide the genealogy of your strains, including full genome alignments and a tree.

VICTOR tool, Virus Classification and Tree Building Online Resource

• Results are sent by e-mail.

Single gene tree tool

• Can calculate tree, similiraties or both.

Ease of use

GGDC tool

• Every step has a question mark o help you go through it.
• Add the accession numbers of each of your genomes.
• Add our e-mail to be noified of the result.

TYGS tool

• Add your genbank or fasta genomes, or add the accession number of your genomes.
• Optionally provide close related species. This is done automaticly.
• Add our e-mail to be noified of the result.

VICTOR tool

• Need to select amino acid or nucleotide (No preselection).
• Enter genebank accession number of your genomes of interest in list, one per line.
• Enter your e-mail to get the result. Results sent in PDF.

Single gene tree tool

• Every step has a question mark o help you go through it.
• Add the accession numbers of each of your genomes.
• Add our e-mail to be noified of the result.

Help

• General Help FAQ Page {.links-list}

GGDC tool

• GGDC Help FAQ Page {.links-list}

TYGS tool

• TYGS Help FAQ Page {.links-list}

VICTOR tool

• VICTOR Help FAQ Page {.links-list}

Single gene tree tool

• Phylogeny Tool Help FAQ Page {.links-list}

Citation

GGDC tool

• Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P., & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics, 14(1), 60. {.grid-list}

TYGS tool

• Meier-Kolthoff, J.P., Göker, M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 10, 2182 (2019). {.grid-list}

VICTOR tool

• Meier-Kolthoff, J. P., & Göker, M. (2017). VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics, 33(21), 3396-3404. {.grid-list}