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GET_HOMOLOGUES specifications


Unique identifier OMICS_05365
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


No version available

Publications for GET_HOMOLOGUES



GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan Genome Phylogenies, Used for a Critical Geno Taxonomic Revision of the Genus Stenotrophomonas

Front Microbiol
PMCID: 5938378
PMID: 29765358
DOI: 10.3389/fmicb.2018.00771

[…] Smc genomes analyzed in this study. The resulting cgANIb matrix was then converted to a distance matrix (cgANDb = 100%–cgANIb) and clustered with the aid of the script from the GET_HOMOLOGUES suite. Figure shows the resulting cladogram, which resolves 16 clusters within the Smc at a conservative cgANDb cutoff value of 5% (cgANIb = 95%). At this distance level, the four geno […]


Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis

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

[…] 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 sub […]


Complete Genome Sequences of Seven Vibrio anguillarum Strains as Derived from PacBio Sequencing

Genome Biol Evol
PMCID: 5905569
PMID: 29635365
DOI: 10.1093/gbe/evy074

[…] esent 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 7,66 […]


Comparative Genomic Insights into Endofungal Lifestyles of Two Bacterial Endosymbionts, Mycoavidus cysteinexigens and Burkholderia rhizoxinica

PMCID: 5877345
PMID: 29540638
DOI: 10.1264/jsme2.ME17138
call_split See protocol

[…] HASTER) 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) (). […]


Genomic insights into the broad antifungal activity, plant probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6

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

[…] retrieved 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 co […]


Two Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms

Genome Biol Evol
PMCID: 5888409
PMID: 29617810
DOI: 10.1093/gbe/evy059

[…] To compare the pangenomes of the NAPCR1/ST54 and NAP1/ST01 isolates and to facilitate MGE detection, Roary () and Get_Homologues () were used to predict unique gene clusters. A unique gene cluster was defined a group of genes found only in a certain isolate. Additionaly, Roary was employed to estimate the size of […]


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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


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Bruno Contreras-Moreira

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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


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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.