RepeatModeler statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RepeatModeler

Tool usage distribution map

This map represents all the scientific publications referring to RepeatModeler per scientific context
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Associated diseases

This word cloud represents RepeatModeler usage per disease context

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RepeatModeler specifications


Unique identifier OMICS_19729
Name RepeatModeler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Open Software License v. 2.1
Computer skills Advanced
Version 1.0.10
Stability Stable
RepeatMasker & Libraries, RECON, RepeatScout, TRF, NSEG, RMBlast, ABBlast/WUBlast
Maintained Yes




No version available

RepeatModeler citations


Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] i et al., ) and others were also obtained by BLAST search against the Rfam database.The RepeatMasker (Chen, ), RepeatProteinMask (, Tendem Repeats Finder (TRF) (Benson, ) and RepeatModeler (Smith and Hubley, ) were performed to identify repetitive sequences through homolog and de novo prediction. The RepeatMasker and RepeatProteinMask were used to screen the A. ipaensis ge […]


Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115
call_split See protocol

[…] were identified following the standard Maker-P recipe (, accessed October 2015) as described on the GMOD site: (i) RepeatModeler with Repeatscout v1.0.5, Recon v1.08, RepeatMasker version open4.0.5, using RepBase version 20140131 () and TandemRepeatFinder; (ii) GenomeTools LTRharvest and LTRdigest (); (iii) MITEhu […]


Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] Repetitive regions were masked prior to gene prediction. Repeats were modelled ab initio using RepeatModeler v1.0.5 []. Repeats arising from duplicated genes or recent gene family expansions (e.g., alpha-tubulin in R. magnacalcarata []) were removed from the custom repeat library by comparing e […]


Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

PLoS One
PMCID: 5915685
PMID: 29689067
DOI: 10.1371/journal.pone.0196303

[…] generate scaffolds. The generated genome assembly was deposited at GenBank under accession no. MVNS00000000.Repetitive DNA elements were predicted with a combination of RepeatMasker version 4.0.5 and RepeatModeler version 1.0.8. To predict gene structures, Augustus version 3.1 [], SNAP version 2013-11-29 [], GeneMark-ES version 2.3c [], and MAKER2 version 2.31.8 [] were used in combination. August […]


Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality

Proc Natl Acad Sci U S A
PMCID: 5939082
PMID: 29678829
DOI: 10.1073/pnas.1719622115

[…] sing methods as described in SI Appendix, section 1.4. We searched transposable elements in the tea plant genome by integrating de novo methods and homology-based methods with the prediction programs RepeatModeler (, LTR_FINDER (), RepeatMasker (, and RepeatProteinMask (version 3.3.0; Based on th […]


Inter genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum

BMC Genomics
PMCID: 5907747
PMID: 29673315
DOI: 10.1186/s12864-018-4612-2

[…] The assembled genome was annotated using the MAKER (version 2.30) [] annotation pipeline with RepeatMasker (version 4.0.5) []. A F. venenatum specific repeat library was constructed using RepeatModeler (version 1.0.7) and supplied to MAKER for the repeat masking step. Gene calls were generated using FGENESH (version 3.1.2) [] using the Fusarium matrix, AUGUSTUS (version 2.7) [] using F […]

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RepeatModeler funding source(s)
Supported by the NIH (R44 HG02244 and R01 HG002939) and the Institute for Systems Biology.

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