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Protocols

HOGENOM specifications

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Unique identifier OMICS_05353
Name HOGENOM
Restrictions to use None
Maintained Yes

Subtool


  • SiLiX

Publication for HOGENOM

HOGENOM citations

 (21)
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

[…] 1/dryad.pv6df. This dataset consists of 1099 gene families from 39 cyanobacteria species along with a well-resolved dated species tree. To construct the dataset, the gene families were retrieved from HOGENOM [] and multiple alignments were performed on these families with Muscle []. For each alignment, an MCMC sample of at least 3000 trees was obtained with PhyloBayes [] and used to reconstruct an […]

library_books

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

2017
Genome Biol Evol
PMCID: 5739047
PMID: 29220487
DOI: 10.1093/gbe/evx255

[…] Based the 47 complete genome sequence data set, we built a database of homologous gene families following the model of Hogenom databases (). All annotated protein coding sequences (CDSs) were extracted and translated into protein sequences on which a all-versus-all pairwise BLASTP similarity search was performed to bu […]

call_split

SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

2016
Genome Biol Evol
PMCID: 5010899
PMID: 27401173
DOI: 10.1093/gbe/evw165
call_split See protocol

[…] upplementary fig. S1 for topology, Supplementary Material online). We rooted our trees using TPMS () and a reference species tree built with BIONJ () from a distance matrix of the complete genomes of HOGENOM V6 database (). […]

library_books

The link between orthology relations and gene trees: a correction perspective

2016
PMCID: 4833969
PMID: 27087831
DOI: 10.1186/s13015-016-0067-7

[…] plore the link between relations and trees in the perspective of relation and tree correction. Several gene tree databases from whole genomes are available, including for instance Ensembl Compara [], Hogenom [], Phog [], MetaPHOrs [], PhylomeDB [], Panther []. However, due to various limitations such as alignment errors, systematic artifacts of inference methods or insufficient differentiation bet […]

library_books

A computational interactome and functional annotation for the human proteome

2016
eLife
PMCID: 5115866
PMID: 27770567
DOI: 10.7554/eLife.18715.074

[…] t in another (). Detecting orthologous relationships is a complex problem, and a range of methods have been developed with corresponding results compiled into databases, including KEGG (), EggNOG (), Hogenom (), OMA (), OrthoDB (), Ensembl Compara (), Gopher () and InParanoid (). In an attempt to select the most informative method, we trained a Bayesian network on each of these eight databases and […]

library_books

Reconstructing a SuperGeneTree minimizing reconciliation

2015
BMC Bioinformatics
PMCID: 4602317
PMID: 26451911
DOI: 10.1186/1471-2105-16-S14-S4

[…] cally applied to the construction of species trees, they can be used as well for the purpose of constructing gene trees. Several gene tree databases are available (see for example Ensembl Compara [], Hogenom [], Phog [], MetaPHOrs [], PhylomeDB [], Panther[]). For a gene family of interest, many different gene trees can therefore be available, and finding one single supertree displaying them all l […]


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HOGENOM institution(s)
Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard - Lyon 1, Villeurbanne, France

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