GET_HOMOLOGUES protocols

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GET_HOMOLOGUES specifications

Information


Unique identifier OMICS_05365
Name GET_HOMOLOGUES
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publications for GET_HOMOLOGUES

GET_HOMOLOGUES in pipelines

 (13)
2018
PMCID: 5799301
PMID: 29403020
DOI: 10.1038/s41598-018-20889-x

[…] coding sequences (±sd 80) for an average genome size of 1.77 mbp (±sd 0.06 mbp). no plasmids were detected when queried against the plasmidfinder database. orthomcl-based clustering executed in get_homologues estimated a core genome size of 1,271 genes (67% ± sd 3% of the total number of genes), a soft-core size (defined as orthologous genes found in all or all but one of the studied […]

2018
PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] ], we decided to involve them in this study to acquire richer information on the evolution and forces for genome changes of the group due to their relatively unique living strategies., the program get_homologues v3.0.3 [], with three popular clustering algorithms, i.e. bidirectional best hit (bdbh), cogtriangles [] and orthomcl [], was used for clustering orthologous genes and identifying […]

2017
PMCID: 5216340
PMID: 28057934
DOI: 10.1038/srep40206

[…] and assembled using spades 3.6.2. the final assemblies were filtered to contain ≥200 bp contigs. genome annotation was performed using prokka 1.11. pan genome analysis was performed by get_homologues software, using the standard described by tettelin and collaborators., the whole genome sequences of 17 strains achieved from our study and 42 strains available in ncbi genome database […]

2017
PMCID: 5289962
PMID: 28217118
DOI: 10.3389/fmicb.2017.00132

[…] 0.18.3; galili, )., the genetic potential of individual leuconostoc lineages that were identified by the pan-/core-genome analysis was investigated by producing intra-linage pan-genomes using get_homologues (version 2.0.10). the pan-genome for each lineage was analyzed using blast2go v4 (conesa et al., ) to identify functionality, and geneious 8.1.8 (kearse et al., ) to identify sequence […]

2017
PMCID: 5306281
PMID: 28261241
DOI: 10.3389/fpls.2017.00184

[…] genes include several examples of unknown functions, specific transposases or proteins such as prolamins, self-incompatibility s1 or c1 proteins., the results presented in this paper illustrate how get_homologues-est can be used to analyze plant pan-genomes from either genomic sequences or expressed tags. our approach overcomes some intrinsic caveats, such as incomplete sequences or transcripts […]


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GET_HOMOLOGUES in publications

 (50)
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] we developed get_phylomarkers, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (pgm), computed by get_homologues. in the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. multiple sequence alignments […]

PMCID: 5893858
PMID: 29657968
DOI: 10.1128/mSystems.00198-17

[…] analysis and at the centre d’innovation génome québec et université mcgill. all of the genomes were annotated with the rast server () and figfam release 70., the annotated genomes were analyzed with get_homologues () (v.2.0) to identify the core genome and pangenome by the cogtriangle () method for bidirectional best-hit determination. the comparison of the m. florum strains and m. capricolum […]

PMCID: 5905569
PMID: 29635365
DOI: 10.1093/gbe/evy074

[…] in nb10 are also present in all others strains. however, the brig analysis does not display sequences not found in nb10. to add more information we therefore calculated the pan genome using the get_homologues tool (). the orthomcl algorithm was used with default parameters and the 11 complete genomes as input. in brief, the numbers from get_homologues suggest that the pan genome include […]

PMCID: 5877345
PMID: 29540638
DOI: 10.1264/jsme2.ME17138

[…] was used to identify prophage sequences within the genome (, ). detailed pan-genome analyses were performed at the protein level using a bidirectional best-hit (bdbh) algorithm implemented in get_homologues (ver. 2.0.23), imposing a minimum pairwise alignment coverage of 75.0% with default parameters () and visualized using the circos circular visualization data tool (ver. 0.69) ()., […]

PMCID: 5851621
PMID: 29538430
DOI: 10.1371/journal.pone.0194088

[…] and used for a further phylogenetic analysis (closely related genomes in ). as previously described, putative orthologous genes among the 122 genomes plus svbp6 strain were identified using get_homologues package. six hundred and seventy-six clusters of orthologous genes were found and subsequently aligned and trimmed using clustalo v1.2.0 and gblock, respectively. blocks were finally […]


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GET_HOMOLOGUES institution(s)
Estación Experimental de Aula Dei (EEAD-CSIC), Zaragoza, Spain; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico

GET_HOMOLOGUES reviews

 (2)
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Bruno Contreras-Moreira

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Desktop
After reading sro's review, just wanted to add that Alvaro Rodriguez and me have recently tested length normalization as done by OrthoFinder. You can find the results at https://github.com/eead-csic-compbio/get_homologues/tree/master/user_utils/normalize

sro

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Desktop
This suit allows users to calculate pan- and core-genome for prokaryote and eukaryote genomes. It is relatively easy to use and it comes with good tutorials. It allows you to to use different algorithm to calculate orthologues genes, which I like. Moreover is periodically patched and new features are added. Moreover, it is quite interesting the features of looking for syntenic genes only, or look for orthologues intergenic regions. I would only have like to see OrthonFinder implemented and some more visualization tools for syntenic orthologues genes and pan- core-genomes. Overall it is a relly good and flexible tool! Highly recommendable.