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ecceTERA specifications

Information


Unique identifier OMICS_11257
Name ecceTERA
Alternative name TERA
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Version 1.2.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Celine Scorvacca

Information


Unique identifier OMICS_11257
Name ecceTERA
Alternative name TERA
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.2.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Celine Scorvacca

Publications for ecceTERA

ecceTERA citations

 (5)
library_books

GATC: a genetic algorithm for gene tree construction under the Duplication Transfer Loss model of evolution

2018
BMC Genomics
PMCID: 5954287
PMID: 29764363
DOI: 10.1186/s12864-018-4455-x

[…] f the time consistency requirement is relaxed [–]. Due to this reasonable time-complexity, some recent phylogenetic softwares have extended the gene family evolution model to transfers (MowgliNNI [], ecceTERA [], TreeFix-DTL []). Continuous effort is also made for developing fast probabilistic frameworks capturing HGT events (see [] for a review of these models).Integrative methods report gene tre […]

library_books

Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont

2018
Mol Biol Evol
PMCID: 5913679
PMID: 29554291
DOI: 10.1093/molbev/msy029

[…] We used ecceTERA () to compute the most parsimonious number of gene duplications, losses, and transfers to reconciliate a given gene tree with the species tree. All gene families missing in N. CALU 996 but re […]

library_books

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)

2017
BMC Evol Biol
PMCID: 5664452
PMID: 29089018
DOI: 10.1186/s12862-017-1064-2

[…] the gene were deleted in different descendants). To test whether CEG gene trees are significantly less congruent with the species tree compared to non-CEGs we performed a reconciliation analysis with ecceTERA []. This analysis showed that a higher number of gene duplications, losses and transfers are required to reconcile CEG gene trees with the species tree compared to non-CEG gene trees (Kolmogo […]

library_books

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

2017
Genome Biol Evol
PMCID: 5441342
PMID: 28402423
DOI: 10.1093/gbe/evx069

[…] s novel capabilities, including the Boltzman–Gibbs sampling of ancestral adjacencies in the presence of transfers from error-prone/partial genome assemblies. The integration with the software package ecceTERA dedicated to reconciliations () adds novel features, such as the possibility of taking unrooted gene trees or undated species trees as input. As a novelty, it also fully handles gene orientat […]

library_books

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

2017
PMCID: 5386878
PMID: 28235827
DOI: 10.1534/g3.116.038448

[…] e events. Published comparisons of the results from Notung and Ranger-DTL show that phylogeny-based methods for detecting LGT events often give high rates of false-positive results (; ). The software ecceTERA () includes a gene tree correction method that aims to reduce the number of false-positives. EcceTERA results on trees containing only best reciprocal blast orthologs were compared to trees c […]

Citations

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ecceTERA institution(s)
ISE-M, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada; ELTE-MTA “Lendület” Biophysics Research Group, Budapest, Hungary; CNRS/Inria AMIB, Ecole Polytechnique, Palaiseau, France; Institut de Biologie Computationnelle (IBC), Montpellier, France

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