ABGD statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ABGD
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Tool usage distribution map

This map represents all the scientific publications referring to ABGD per scientific context
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Protocols

ABGD specifications

Information


Unique identifier OMICS_30538
Name ABGD
Alternative name Automatic Barcode Gap Discovery
Interface Web user interface
Restrictions to use None
Input data The approximate maximum prior intraspecific distance.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Guillaume Achaz

Additional information


http://wwwabi.snv.jussieu.fr/public/abgd/

Information


Unique identifier OMICS_30538
Name ABGD
Alternative name Automatic Barcode Gap Discovery
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The approximate maximum prior intraspecific distance.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Guillaume Achaz

Additional information


http://wwwabi.snv.jussieu.fr/public/abgd/

Publication for Automatic Barcode Gap Discovery

ABGD citations

 (155)
library_books

Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations

2018
PLoS One
PMCID: 5919620
PMID: 29698411
DOI: 10.1371/journal.pone.0195833

[…] tric tree in BEAST software v. 1.8.3 [] with 600,000 MCMC generations, 100 thinnings and a burn-in of 6,000. This tree was used as input to GMYC. The COI sequences also were used in the web server of Automatic Barcode Gap Discovery for primary species delimitation software (ABGD, http://wwwabi.snv.jussieu.fr/public/abgd/abgdweb.html) [] with default conditions, to complement the species delimitati […]

call_split

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes)

2018
Front Genet
PMCID: 5893770
PMID: 29670644
DOI: 10.3389/fgene.2018.00107
call_split See protocol

[…] . We used a nexus MCC tree generated in Beast 1.8.0 (Drummond et al., ) as input file and ran 500,000 generations (thinning = 500). We also used a clustering species delimitation analysis through the Automatic Barcode Gap Discovery (ABGD; Puillandre et al., ) that automatically defines sequences into hypothetical candidate species based on confidence limits for intraspecific divergence. We used a […]

library_books

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

2018
BMC Evol Biol
PMCID: 5883351
PMID: 29614961
DOI: 10.1186/s12862-018-1160-y

[…] istinguish between intraspecific and interspecific variation, sometimes referred to as the “barcoding gap” []. Several programs and software packages determine and visualize barcoding gaps, including Automatic Barcode Gap Discovery (ABGD) [] and Spider []. These distance-based methods are fast and suitable for large datasets, but they are not always biologically meaningful, especially when the spe […]

library_books

Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages

2018
PLoS One
PMCID: 5854346
PMID: 29543844
DOI: 10.1371/journal.pone.0194045

[…] among different species groups of Daphnia (see [,]). Although we detected two highly distinct mitochondrial super-clades within Daphnia magna, which may be interpreted as separate taxa (e.g., by the ABGD test), several lines of evidence strongly suggest that they represent two divergent super-clades within a single species. First, the genetic distance between the two super clades is much smaller […]

library_books

First true brackish water nudibranch mollusc provides new insights for phylogeny and biogeography and reveals paedomorphosis driven evolution

2018
PLoS One
PMCID: 5851531
PMID: 29538398
DOI: 10.1371/journal.pone.0192177

[…] TCS network method. The program Mega7 [] was used to calculate the minimum uncorrected p-distances between all the sequences. Intra- and intergroup genetic distances were also examined.Additionally, Automatic Barcode Gap Discovery (ABGD) [] was used to define species. Alignment from the COI marker for Bohuslania, Cuthona, and Tenellia specimens were submitted and processed in ABGD using the Jukes […]

library_books

Molecular taxonomy and evolutionary relationships in the Oswaldoi Konderi complex (Anophelinae: Anopheles: Nyssorhynchus) from the Brazilian Amazon region

2018
PLoS One
PMCID: 5837296
PMID: 29505595
DOI: 10.1371/journal.pone.0193591

[…] e []. Successful identification was determined based on the 1% standard threshold cut-off, as suggested by The Barcode of Life Data System as barcoding satisfactory gap to delimit cryptic species []. Automatic Barcode Gap Discovery (ABGD) analysis allowed partitioning of the DNA sequence datasets into clusters of similar taxa, establishing a range of maximum values of intraspecific divergence (P), […]


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ABGD institution(s)
UMR 7138, Museum National d’Histoire Naturelle, Departement Systematique et Evolution, Paris, France; Laboratoire de Probabilites et Modeles Aleatoires (UMR 7599), UPMC Univ Paris 06, Univ Paris Diderot, CNRS, Paris, France; Systematique, Adaptation et Evolution (UMR 7138), UPMC Univ Paris 06, CNRS, MNHN, IRD, Paris, France; Atelier de Bioinformatique, UPMC Univ Paris 06, Paris, France
ABGD funding source(s)
Supported by grant 07-GMGE-004-04 from the Agence Nationale pour la Recherche (French national research agency) and by the JSPS for a long-term fellowship for research in Japan FY2009; by projects BLAN06-3_146282 MAEV and NT09_545511 MANEGE of Agence Nationale pour la Recherche and by a postdoctoral fellowship from the Centre National de la Recherche Scienfitique.

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